Sorry about replying so late; missed the notification email, apparently.
I cannot really tell what version of the plugin the reference builds used. I don't think I was far behind on the upgrades, but it could have been a month or two ... 4.6 was the newest when I upgraded.
Here are some console output snippets:
First we have build #760 of jobA:
Build done
[WARNINGS] Parsing warnings in files 'jobres*.txt' with parser MSBuild
[WARNINGS] Parsing 1 files in S:\jenkins\workspaces\jobA
[WARNINGS] Successfully parsed file S:\jenkins\workspaces\jobA\jobresA.txt of module with 28 warnings.
[WARNINGS] Parsing warnings in files 'jobres*.txt' with parser XmlDoc Warnings
[WARNINGS] Parsing 1 files in S:\jenkins\workspaces\jobA
[WARNINGS] Successfully parsed file S:\jenkins\workspaces\jobA\jobresA.txt of module with 313 warnings.
[WARNINGS] Computing warning deltas based on reference build #700
Archiving artifacts
Build #700 is gone by now. Actually things started working as expected as the old builds expired, which backs your incompability statement. It would have been nice, though, if the plugin had chosen no reference instead of one it couldn't use anyway.
Next snippet is from build #284 of jobB:
Build done
[WARNINGS] Parsing warnings in files 'jobresWin.txt' with parser MSBuild
[WARNINGS] Parsing 1 files in S:\jenkins\workspaces\jobB
[WARNINGS] Successfully parsed file S:\jenkins\workspaces\jobB\jobresWin.txt of module with 5 warnings.
[WARNINGS] Parsing warnings in files 'jobresLinux.txt' with parser GNU Compiler 4 (gcc)
[WARNINGS] Parsing 1 files in S:\jenkins\workspaces\jobB
[WARNINGS] Successfully parsed file S:\jenkins\workspaces\jobB\jobresLinux.txt of module with 5 warnings.
[WARNINGS] Computing warning deltas based on reference build #267
[TASKS] Scanning folder 'S:\jenkins\workspaces\jobB' for files matching the pattern '*/.cpp,*/.h' - excludes: build/*,lib/*
[TASKS] Found 53 files to scan for tasks
[TASKS] Found 2 open tasks.
[TASKS] Computing warning deltas based on reference build #283
Archiving artifacts
This one shows that the tasks plugin has a different idea about reference than the warnings plugin.
The reference builds were in both cases (and many more cases) the last build made before upgrading to warnings 4.6.
The problem seems to have "solved" itself as the builds expire, but that only works because we do expire builds...
Can you please add some more details?
E.g. what is printed on the console ([WARNINGS] ...), what is the number of warnings in one of the new builds and the reference build. Is the reference build created with release 3.x?
What changed from 3.x to 4.x: Now each parser has it's own results. I.e. the results of Java warnings are compared to old results of Java warnings. Of course this will lead to wrong results when comparing a 4.x build with a 3.x build.