If you follow the archives you'll find more than one poster who reverted back to
the original CPU and brought back a S900, which then accepted all the upgrades
over again. Electronic quirks can be tough to fix, tougher to explain why it
happened. Paul C
These situations are almost certainly caused by corrupted contents in the NVRAM. The NVRAMrc file is stored there, among other things. The NVRAMrc file is a collection of Open Firmware (tokenized Forth) programs which the computer executes at boot up before it has even started looking for the operating system. The Device Tree is also stored there, which is a tree structure the Open Firmware uses to know which components are installed on the computer. When these things get corrupted or simply contain incorrect information (no data errors, just bad data) it can lead to the machine failing to boot.
In an ideal world, the device tree, at least, would never get munged because the Open Firmware routines that create it would work perfectly. La la la la la....
The NVRAMrc file is more subject to errors because those little programs are loaded in by programs run under the Mac OS (usually by the OS itself or extensions). So a grotty extension can load bogus or inappropriate programs in the NVRAMrc, which will cause the machine to fail at the next boot up.
Fortunately, the NVRAM is physically stored in an SRAM chip which is not truly "non-volatile". It is only non-volatile as long as it has a smidgen of current. Removing the battery and unplugging the machine removes the sources of this current, but there may still be a bit of charge stored up in the capacitors on the motherboard--hence the recommendation to let the machine sit a good long while. SRAM is very good at retaining its contents on a tiny little trickle of electrons.
The before-chime-PRAM-zap I recommended also seems to reset the NVRAM thoroughly, as opposed to just resetting the PRAM as one would expect. (PRAM is another bit of "non-volatile" storage, but it has a different physical location.) However, I suppose it may be possible for a machine's NVRAM to be so hosed that it can't recognize the Uber-Zap. So power removal may be the only viable option in some cases. Personally, I've never run into a case that the Uber-Zap wouldn't correct.
Jeff Walther
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