Do the "non-listening" base stations show up on the port card status at all, or do they not even register?
Have you taken non-listening base stations and swapped them out with ones that are working to see if they come up in those locations? If you move the non cooperative ones and they work then you can probably assume they are OK - test out all your bad ones this way for peace of mind. If the bad ones don't work in the good locations then the base stations are probably fried.
Just for giggles, if you find bad base stations and don't have a service contract, and you are using only 1 power pair, try punching down your power pair to one of the other 2 pairs on the cable running out to the base station. If by chance each of the 3 power pairs on the base station is independently protected you may be able to get around having to replace them.
If all of your "bad" base stations work when moved to working locations, the next stop is the card in the system. Each card has 2 power supply channels - one for each of 3 base stations.
If no base stations are working at all on a card then the card might be fried. If any base stations are working at all - especially if more than one on a card, suspect one power channel. If you have at least one base station working on each power channel of a card then assume the card is OK. If all the ones working are on one channel and none on the other, or if none are working at all, roll that card with one of the other ones that is known to be working better and see if it improves anything. If it does suspect the board again.
The last place I would probably head to is the power supply. The 3000 has weird power requirements, and requires different amounts of input power depending on how much load you are putting on it. I have a reltek power supply that has 3 separate outputs that can be paralleled together to increase the available amps/watts/whatever, but only use 2 of them right now - I have 4 station/base station cards plus the CPU and that works fine for me. If your power supply is damaged and is putting out the rated voltage but not the rated current the 3000 will still work, but will just be power-starved. I would assume the base stations furthest cable-wise from the system would be the most effected - especially if you're only running one power pair out to them.
Hopefully this gives you some places to look further.