I have an old A1200 with a rewired PC supply and I have had similar problems in the past. In my case I discovered that the problem was inside the Amiga. I had wired all my additional internal goodies to the same plug that supplies the floppy drive et al. The problem is that this connector is not very secure and makes bad contact. In addition when the machine draws a big current load (such as at bootup) the small plug just can't deliver, especially if the connection is also dodgy (as in my case). I guess the solution would be to change the plug and put in a heavier duty one, but that would involve a lot of soldering and my motherboard is already tired and covered in my amateur solder jobs, so for now I just wiggle the connector from time to time when I have a problem and it goes back to normal for a while. Your milage may vary ....
