I noticed a case in which the warnings surrounding a modified line are not shown as "new warnings". But according to: https://issues.jenkins-ci.org/browse/JENKINS-6675 they should be shown because the warnings are within +/-3 line of the modified line. I assume that the warnings plugin is taken the modified lines from the SCM.

The file was changed in line 77 (see 4) but the surrounding warnings (see 1) are not shown in the "New warnings" (see 2).
1) The warnings: http://jenkins.gromacs.org/view/Gerrit%20Docu/job/Doxygen_Gerrit_master/65/warningsResult/package.689474037/file.-1578484055/
2) 0 new warngins: http://jenkins.gromacs.org/view/Gerrit%20Docu/job/Doxygen_Gerrit_master/65/warningsResult/new/
3) Showing that the file was changed: http://jenkins.gromacs.org/view/Gerrit%20Docu/job/Doxygen_Gerrit_master/65/changes#detail0
4) Showing the diff for the file: https://gerrit.gromacs.org/#/c/517/13/src/gromacs/trajectoryanalysis/runnercommon.h

Maybe interesting the new warning detection did work correctly with an earlier reference build.
For that build, the new warnings were detected correctly: http://jenkins.gromacs.org/view/Gerrit%20Docu/job/Doxygen_Gerrit_master/59/warningsResult/new/package.689474037.
The file changed exactly the same for build 59 and build 65.

The plugins and Jenkins is the latest version.

Please let me know if I can provide any further information.