I have a similar issue with the latest free version I installed a few days ago (2014.9.0.2011).
When I start programs, they seem to start up slowly , and then splash off as if they have shut down, and then open up again a second or two later. The most annoying thing is that any changes I make when they first appear are lost when they re-appear.
This doesn't affect all programs, just quite a lot of them. If I disable AV for ten minutes on the tray icon, it doesn't happen.
Windows XP SP3