@Tuxedo

In the beginning of the release of the Pegasos2, I recall I needed to use following flash update : http://www.bplan-gmbh.de/output.php?PAGE_ID=162&nid=16

Maybe there's a newer one aswell but that's more than I know of.

Dunno if this can solve your problem, it sounds more like it's a stuck PLL but you never know until you tested =)
Compability shall be uneffected, you might want to check the env-variables before you flash the board so you can apply it again so the system boots correct boot file etc.

@Tuxedo

To satisfy my curiosity about something, could you run the following simple program in both OS4 and MorphOS on your machine before you fiddle with any hardware/firmware settings?

See here

The provided executable is for 68K and has been already tested on two different spec A1200's and OS4.1 on a G4 800.

It should take almost exactly 10 seconds to run, so for added validation, check it against a real stopwatch ;)

Hopefully, the reported time in the last line of the output should be 10 seconds, give or take a few hundredths...

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Doing stupid things for fun...