The problem is caused by PM rescanning the folder(s) after a application change. It does that to be able to recognize any changes made to files (outside PM). Both PM5 and PM6 do this, but the way (when) sorting results are shown is different. Overall PM6 should actually be faster, but the new method has some drawbacks too (Kirk should be able to explain this way better, I think).
What sorting method do you use? Filename is fastest and should be on par with PM5. File modification is also quite fast, but most other require the file to be analysed for metadata and that always causes a delay, so sticking to filename is usually the best.