Steps to reproduce:
1. Create new workspace.
2. Create new java project.
3. Add the class attached to the issue.
4. Go to Window->Preferences->PMD->Rule Configuration
5. Switch on "Use global rule management"
6. Select each of two rules "Empty Catch Block" and mark "Empty blocks containing comments will be skipped" on "Properties" page.
7. Remove mark from rule "LocalVariableCouldBeFinal".
8. Apply changes.
9. Open context menu in added class editor and select PMD->Check Code.
10. Sure that the problem "LocalVariableCouldBeFinal" was not reported.
11. Clear violations (PMD->Clear Violations)
11. Restart Eclipse
12. Open context menu in added class editor and select PMD->Check Code.
13. Sure that the problem "LocalVariableCouldBeFinal" WAS reported. BUT it is not expected!
14. Open PMD global rule configuration and sure that rule "LocalVariableCouldBeFinal" is switched off.
15. Place and remove mark on the rule, remove violations and check code again. The problem is not reported anymore.
Eclipse: Eclipse IDE for Java EE Developers Eclipse IDE for Java EE Developers x64 4.3.2
OS: Windows 7 x64
I think, I've fixed it. You can try out the fix by installing the latest (snapshot) version of the plugin from here:
https://sourceforge.net/projects/pmd/files/pmd-eclipse/update-site-latest/
The bugfix will be included in the next release of the plugin.