Do you have rlog output and the name of the branch you're building against? We don't apply -r since CvsLog does filtering according to version numbers so should filter out the changes we're not interested in.

Please see attached file JENKINS-15416.zip .
As you can see in included file hyperdoc-buildresources-HEAD\config.xml the HEAD is selected.
The pollingLog file mentions a sourcecode change.
The changes.htm shows one changed file /iqdoq/product/hyp4x/build/versno.properties with revision no 1.1307.2.18.2.41 .
To verify that this revision was not checked in to the Head (branch) please see the screenshot file viewvc_screenshot_shows_commit_is_on_branch_hyp-5-3-1-branch_and_not_HEAD.png . The commit was done in branch hyp-5-3-1-branch (not HEAD).

Also in jenkins.log I am getting numerous warnings like "#65188 warning C/S protocol error (section 5.10). It's regurarly observed with cvs 1.12.xx servers.".

I have copied the job hyperdoc-buildresources-HEAD for the build of another branch (hyp-5-4-0-branch). I have named the job hyperdoc-buildresources-5-4-0
If a commit is done out of that hyp-5-4-0-branch, the job hyperdoc-buildresources-5-4-0 detects no scm changes.
This leads me to the assumption that the scm changes detector only has problems if the job uses the CVS Head.

Perhaps the logic has to be changed that when Head is selected the changes detector has to filter out all branches rather than include a specific branch?

The "It's regurarly observed with cvs 1.12.xx servers" warnings are your CVS server not following the CVS protocol properly (they don't set the path to CVS root in their response) and can be safely ignored if you're not having issues (I think we'd have to modify CVS Client if we wanted to prevent this message completely).

Are you able to provide the output of the rlog command for the period you were building? Feel free to obfuscate any sensitive values (repository names, paths, filenames etc) if needed. This would help greatly in recreating the issue and adding unit tests to prevent it re-occurring. Also, what comment is shown against the change if you select it on the changes page? Is it 'xxxx was originally added on branch xxxx'?

Please see attached file cvs_rlog_out_hyperdoc-buildresources-HEAD-3.txt .

I have simply 'replayed' the CVS rlog output command like that on the linux jenkins master command line:
cvs rlog -S -d"05 Oct 2012 11:00:41 +0200<05 Oct 2012 16:00:53 +0200" iqdoq/product/hyp4x/build 2>&1> cvs_rlog_out_hyperdoc-buildresources-HEAD-3.txt

The comment on the changes page is:
Änderungen
Zusammenfassung

Autobuild: Release build hyp-5-3-1-28_442

autobuild:
Autobuild: Release build hyp-5-3-1-28_442
The file was modified 1.1307.2.18.2.41 /iqdoq/product/hyp4x/build/versno.properties