I agree with you, and that's why I feel helpless about this situation.Unusual sort of failure, definitely. Please update the list on what the problem turns out to be when you track it down. If it's sufficiently weird I'll add it to the notes. :)
Some random thoughts:
1) If the electrolytics in the 100V/300V multiplier sections on the power supply board are bad, there might be enough ripple coming through to confuse a DMM. The load on the supply may affect this behavior. Try a different meter if possible, and see if you get the same unintuitive measurements out of it. I know you replaced the caps, but sometimes the new ones are bad too.
2) It doesn't normally make sense for the green light to be on while the rail voltages are incorrect. Taking a close look at the comparator circuit that drives the LED might provide some insight. The +300V rail isn't monitored by that circuit, but +100V is.
3) I'm not sure what documentation is available on the 492B models. It would be best to consult the 494A manuals available at ko4bb.com, IMHO. Those are the latest editions for the 49x series that were published as far as I'm aware. They have quite a few change notes in the back that may apply to your unit.
-- john, KE5FX