If I'm using the Perforce plugin and have a setting for this project
(FPHibernate-Head) with a workspace like this:
Single Workspace: wyliek.hudson-clients.fphibernate-head.london
View: //fotech/shared/lib/java/FPHibernate/head/...
Hudson Home: /scratch/betasx2/wyliek/hudson-home

And am using a configuration matrix of jdk1.6.0_03 and jdk1.5.0_13, what seems
to happen is this:
1) Perforce plugin does a sync to
/scratch/betasx2/wyliek/hudson-home/jobs/FPHibernate-Head/workspace
2) Matrix runner creates axis directory of
/scratch/betasx2/wyliek/hudson-home/jobs/FPHibernate-Head/workspace/jdk/jdk1.5.0_13
3) Perforce Plugin changes the root of the workspace to
/scratch/betasx2/wyliek/hudson-home/jobs/FPHibernate-Head/workspace/jdk/jdk1.5.0_13
and does a p4 sync. P4 says nothing to sync, but there's nothing there.
4) Ant doesn't find the build.xml file to run.

Here's the output on the overall project running:
started
Performing sync with Perforce for: //fotech/shared/lib/java/FPHibernate/head/...
Changing P4 Client Root to:
/scratch/betasx2/wyliek/hudson-home/jobs/FPHibernate-Head/workspace/
Changing P4 Client View to: //fotech/shared/lib/java/FPHibernate/head/...
//wyliek.hudson-clients.fphibernate-head.london/...
Last sync'd change: 76672
Sync'ing workspace to depot.
ForceSync flag is set, forcing: p4 sync
//fotech/shared/lib/java/FPHibernate/head/...
Sync complete, took 3392 MS
Triggering jdk=jdk1.6.0_03
Triggering jdk=jdk1.5.0_13
finished: FAILURE

Here's the output on the jdk1.6.0_03 axis run:
started
Performing sync with Perforce for: //fotech/shared/lib/java/FPHibernate/head/...
Changing P4 Client Root to:
/scratch/betasx2/wyliek/hudson-home/jobs/FPHibernate-Head/workspace/jdk/jdk1.6.0_03/
Changing P4 Client View to: //fotech/shared/lib/java/FPHibernate/head/...
//wyliek.hudson-clients.fphibernate-head.london/...
Last sync'd change: 76672
No changes since last build.
[jdk1.6.0_03] $ /scratch/betasx2/wyliek/apache-ant-1.7.0/bin/ant
-Djdk=jdk1.6.0_03 tests
Buildfile: build.xml does not exist!
Build failed
Recording test results
finished: FAILURE

Here's the output on the jdk1.5.0_13 axis run:
started
Performing sync with Perforce for: //fotech/shared/lib/java/FPHibernate/head/...
Changing P4 Client Root to:
/scratch/betasx2/wyliek/hudson-home/jobs/FPHibernate-Head/workspace/jdk/jdk1.5.0_13/
Changing P4 Client View to: //fotech/shared/lib/java/FPHibernate/head/...
//wyliek.hudson-clients.fphibernate-head.london/...
Last sync'd change: 76672
No changes since last build.
[jdk1.5.0_13] $ /scratch/betasx2/wyliek/apache-ant-1.7.0/bin/ant
-Djdk=jdk1.5.0_13 tests
Buildfile: build.xml does not exist!
Build failed
Recording test results
finished: FAILURE