I have no time right to have a look at what might be going behind the scenes (I'll have a look at the code next week).
But here are some suggestions on different ways that might help:
1. You could add the FlexPMD nature to your project. this way every time you compile a project flexpmd would executed incrementally in the modified files
2. You can install a yet-to-be-released version of the plugin from here www.rialvalue.com/flexPmd/updateSite this version has a "FlexPMD outline View" that will list the bugs in the opened file and will update (execute Pmd on the file) every you save it