I use PStart and don't seem to have had any problems with any of the applications running.
However, i do notice the icons in PStart seem to 'float'. eg sometimes the FireFox icon appears next to Thunderbird. Sometimes it seems as many as 6 have floated.
Occasionally the odd desktop icons seem to have floated.
While no-one else to the best of my knowledge has mentioned this i'd be interested to know what a possible cause could be. It didn't happen before i used portable apps so i am just assuming that it is something to do with it!