By timer, do you mean a Blitz timer, or MilliSecs()? The latter should NEVER stop, as it is the number of milliseconds your system has been up (or was it from midnight? One of the two). The idea of Blitz timers stopping when an alt-tab occurs, while nice, sounds like it could be very difficult to implement.
In terms of funny behaviour with the bullets, I think that when in fullscreen mode, flips may not wait for a vertical blank (Vwait may not either) as the screen is not being displayed. That's what I decided problems I had in my game were down to anyway. Which is why I migrated to BlitzPlus, as an event driven system is the only way you can really hope to deal with this (which doesn't help B3ders of course!)
In terms of funny behaviour with the bullets, I think that when in fullscreen mode, flips may not wait for a vertical blank (Vwait may not either) as the screen is not being displayed. That's what I decided problems I had in my game were down to anyway. Which is why I migrated to BlitzPlus, as an event driven system is the only way you can really hope to deal with this (which doesn't help B3ders of course!)