These are just two shots in the dark (as I would have to look up old notes to make it more reliable) - but:
1. Might your Dallas Chip (=RealTimeClock with RAM) Battery be dead? (Same possibility in the replacement CPU board of same age, naturally...)
Suitable replacement ICs are available through ebay from Asia. I remember very vaguely that this solved a similar startup problem on mine maybe a year ago; I may even have posted something about it in this group.
2. Have you tried reseating all the cards? (Power off before that... :-) )