Yeah the alarm trigger thing is a real pain. I only have issues with it when uploading and restoring via card. I have downloaded with a card and never had a problem.
What usually happens when I open the restored project is the alarm set-up editor will be totally scrambled. Messages will be unassigned, or just totally gone, or triggers will be gone.
The guys at RA seem pretty baffled by it when I've talked to them. I'm just hoping that when we go to 6.0 that some of these issues will be resolved...