I have two environemnts wtih two diff jenkins installed.
1. Using Jenkins : ver 1.6907. On this machine I am able to post config.xml on a job using curl api:
curl -v -X POST --data-binary @myconfig.xml -u "userid:apiToken" http://localhost:8080/job/job_name/config.xml

using above, the modified config gets updated in Jenkins.

2. Using Jenkins ver 1.5961:
when I use the same step in the evn, I am seeing an exception:

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<a href="http://jenkins-ci.org/content/mailing-lists">The users list</a> might be also useful in understanding what has happened.</p><h2>Stack trace</h2><pre style="margin:2em; clear:both">java.io.IOException: Failed to persist config.xml
at hudson.model.AbstractItem.updateByXml(AbstractItem.java:648)
at hudson.model.AbstractItem.doConfigDotXml(AbstractItem.java:614)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.kohsuke.stapler.Function$InstanceFunction.invoke(Function.java:298)
at org.kohsuke.stapler.Function.bindAndInvoke(Function.java:161)
at org.kohsuke.stapler.Function.bindAndInvokeAndServeResponse(Function.java:96)
at org.kohsuke.stapler.MetaClass$1.doDispatch(MetaClass.java:121)
at org.kohsuke.stapler.NameBasedDispatcher.dispatch(NameBasedDispatcher.java:53)
at org.kohsuke.stapler.Stapler.tryInvoke(Stapler.java:746)
at org.kohsuke.stapler.Stapler.invoke(Stapler.java:876)
at org.kohsuke.stapler.MetaClass$6.doDispatch(MetaClass.java:249)
at org.kohsuke.stapler.NameBasedDispatcher.dispatch(NameBasedDispatcher.java:53)
at org.kohsuke.stapler.Stapler.tryInvoke(Stapler.java:746)
at org.kohsuke.stapler.Stapler.invoke(Stapler.java:876)
at org.kohsuke.stapler.MetaClass$6.doDispatch(MetaClass.java:249)
at org.kohsuke.stapler.NameBasedDispatcher.dispatch(NameBasedDispatcher.java:53)
at org.kohsuke.stapler.Stapler.tryInvoke(Stapler.java:746)
at org.kohsuke.stapler.Stapler.invoke(Stapler.java:876)
at org.kohsuke.stapler.Stapler.invoke(Stapler.java:649)
at org.kohsuke.stapler.Stapler.service(Stapler.java:238)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at hudson.util.PluginServletFilter$1.doFilter(PluginServletFilter.java:96)
at hudson.plugins.scm_sync_configuration.extensions.ScmSyncConfigurationFilter$1.call(ScmSyncConfigurationFilter.java:36)
at hudson.plugins.scm_sync_configuration.ScmSyncConfigurationDataProvider.provideRequestDuring(ScmSyncConfigurationDataProvider.java:103)
at hudson.plugins.scm_sync_configuration.extensions.ScmSyncConfigurationFilter.doFilter(ScmSyncConfigurationFilter.java:32)
at hudson.util.PluginServletFilter$1.doFilter(PluginServletFilter.java:99)
at net.bull.javamelody.MonitoringFilter.doFilter(MonitoringFilter.java:206)
at net.bull.javamelody.MonitoringFilter.doFilter(MonitoringFilter.java:179)
at net.bull.javamelody.PluginMonitoringFilter.doFilter(PluginMonitoringFilter.java:86)
at org.jvnet.hudson.plugins.monitoring.HudsonMonitoringFilter.doFilter(HudsonMonitoringFilter.java:84)
at hudson.util.PluginServletFilter$1.doFilter(PluginServletFilter.java:99)
at hudson.plugins.audit_trail.AuditTrailFilter.doFilter(AuditTrailFilter.java:66)
at hudson.util.PluginServletFilter$1.doFilter(PluginServletFilter.java:99)
at hudson.util.PluginServletFilter.doFilter(PluginServletFilter.java:88)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at hudson.security.csrf.CrumbFilter.doFilter(CrumbFilter.java:48)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at hudson.security.ChainedServletFilter$1.doFilter(ChainedServletFilter.java:84)
at hudson.security.UnwrapSecurityExceptionFilter.doFilter(UnwrapSecurityExceptionFilter.java:51)
at hudson.security.ChainedServletFilter$1.doFilter(ChainedServletFilter.java:87)
at jenkins.security.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:117)
at hudson.security.ChainedServletFilter$1.doFilter(ChainedServletFilter.java:87)
at org.acegisecurity.providers.anonymous.AnonymousProcessingFilter.doFilter(AnonymousProcessingFilter.java:125)
at hudson.security.ChainedServletFilter$1.doFilter(ChainedServletFilter.java:87)
at org.acegisecurity.ui.rememberme.RememberMeProcessingFilter.doFilter(RememberMeProcessingFilter.java:142)
at hudson.security.ChainedServletFilter$1.doFilter(ChainedServletFilter.java:87)
at org.acegisecurity.ui.AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java:271)
at hudson.security.ChainedServletFilter$1.doFilter(ChainedServletFilter.java:87)
at jenkins.security.BasicHeaderProcessor.success(BasicHeaderProcessor.java:140)
at jenkins.security.BasicHeaderProcessor.doFilter(BasicHeaderProcessor.java:82)
at hudson.security.ChainedServletFilter$1.doFilter(ChainedServletFilter.java:87)
at org.acegisecurity.context.HttpSessionContextIntegrationFilter.doFilter(HttpSessionContextIntegrationFilter.java:249)
at hudson.security.HttpSessionContextIntegrationFilter2.doFilter(HttpSessionContextIntegrationFilter2.java:67)
at hudson.security.ChainedServletFilter$1.doFilter(ChainedServletFilter.java:87)
at hudson.security.ChainedServletFilter.doFilter(ChainedServletFilter.java:76)
at hudson.security.HudsonFilter.doFilter(HudsonFilter.java:164)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at org.kohsuke.stapler.compression.CompressionFilter.doFilter(CompressionFilter.java:49)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at hudson.util.CharacterEncodingFilter.doFilter(CharacterEncodingFilter.java:81)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at org.kohsuke.stapler.DiagnosticThreadNameFilter.doFilter(DiagnosticThreadNameFilter.java:30)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:233)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:558)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:298)
at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:852)
at org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:588)
at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:489)
at java.lang.Thread.run(Thread.java:619)
Caused by: java.lang.ClassNotFoundException: org.apache.xerces.parsers.SAXParser
at org.xml.sax.helpers.XMLReaderFactory.loadClass(XMLReaderFactory.java:189)
at org.xml.sax.helpers.XMLReaderFactory.createXMLReader(XMLReaderFactory.java:150)
at jenkins.util.xml.XMLUtils.safeTransform(XMLUtils.java:48)
at hudson.model.AbstractItem.updateByXml(AbstractItem.java:643)
... 84 more
Caused by: java.lang.ClassNotFoundException: org.apache.xerces.parsers.SAXParser
at org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:1516)
at org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:1361)
at org.xml.sax.helpers.NewInstance.newInstance(NewInstance.java:49)
at org.xml.sax.helpers.XMLReaderFactory.loadClass(XMLReaderFactory.java:187)
... 87 more