I see your problem, now. It could be faulty/dead battery. Batteries can read good voltages without any load on them, but as soon as you load them (the dead batteries, I mean) their voltage will drop, and they will discharge fast. But, I am not really sure about this, because in this case current draw (load) will be very small (in microamps). But then again, if battery is dead, its internal resistance have become high enough to cause significant voltage drop, even with microamps load.
There is also a possibility that there is some extra load (that shouldn't be there) across the battery (besides CMOS RAM, or whatever it is used).
Try with a new battery.
Those electrolytic capacitors you have replaced have nothing to do with that. When they go bad, motherboard will not work at all (due to increased ripple). Make sure that those new caps you have installed are low ESR ones (low equivalent series resistance), otherwise they will cause more ripple, heat up more, and fail in relatively short time.