Refugee,
I think the posts above are correct. I noticed the same thing when I first started using TrackIR 5. Once you minimize AH it looks like TIR has closed, but it is really still open (you can verify this by going back into AH and see that TIR is still working).
I'm running XP so the TIR software icon is located on the bottom right-hand side of my start menu bar. It I double click that icon, i can get back into the TIR software with no problems.
Hopefully that's all it is.
