There is a hardware problem that has surfaced in some falcon's and I don't think there is a known fix. Check this description and see if it fits your falcon's problem.
http://www.atariuk.co.uk/ go to the bug fixes section.
Now, the fact that you can correct it by software makes me think that it may be a software issue, so try booting with the control key pressed and see if the problem is repeatable. And is fpatch2.prg in your auto folder?
