Strange A4000 behavior

[Computolio]

    I have here an Amiga 4000 that seems to work, mostly. The machine boots and runs stuff fine, but any software resets (or crashing) causes the expansion cards to disappear. They won't show up again unless I turn the machine off then on again or do a manual reset. I've found occasional mentions of similar problems on Usnet, but nobody was ever able to figure out what was going on.
    Another oddity is that the power light never dims. It's supposed to start out dim then quickly go bright on startup, and it's supposed to go from bright to dim whenever the audio filter is toggled.
    Could some of this be caused by the suicide battery? It made an amazing mess of the board when it leaked (it's so bad that it's a miracle the machine works as well as it does), and the RTC is dead. Maybe some other circuitry got messed up?

[Computolio]

I replaced the CPU with a full 040. I've also changed out the riser board, but it's no use. Boards are still disappearing after software resets.

     A search on Usnet reveals that at least a couple of other people have had this problem, but nobody was able to solve it. Has anyone here run into this problem?

[gdanko]

Wow that's a new one to me. Tower or desktop?

[Tahoe]

What revision Buster and Kickstart does it have?

Are you really sure on the LED behaviour? On an A4000 I find it much harder to notice then on an A1200 for instance.

[Computolio]

    Buster is rev. 11, Kickstart is 3.1.

    I am pretty sure on the LED behavior, as I can't notice any change while toggling the filter.