I couldn't find the original post but I recall some of you having this problem in the past. At the time I was unable to reproduce the problem though I made a few changing thinking it would solve the problem. It didn't.
Today my webmaster came to me and told me FlashFXP was still having this problem. He offered to spend some time and help me uncover the problem.
We're both using Win2k with all the latest patches though flashing worked for me and not him most of the time. After an hour or so of testing I finally added the right debug message which pointed to the problem.
The problem was with using the WM_ACTIVATEAPP to determine if the application was active, for some reason it was reporting the wrong result.
So I worked around the problem and then he tested it again, success
, it would appear the problem has finally been solved.
Unfortunately this was hours after just releasing the latest public beta update, so you'll have to wait
for the next update.