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From an OS perspective this doesn't matter since the AGP port is connected as PCI.
Actually it does because X.org drivers are stupid and check the card capabilities based on chipset, configuration space and *expected* bus combinations, not the ACTUAL PHYSICAL bus on the system.
So if you plug an AGP chipset into a PCI board, X.org swizzles it and thinks, oh this is an AGP chipset and says it's capable of supporting AGP (and probably hundreds of other impossible features), I will try setting up the AGP GART on it, and BOOM.
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That's why xorg.conf must contain BusType PCI.
Make sure you have that line somewhere.
In theory his card should just work, Radeon PCI are known as Radeon PCI to X.org. I'm not too sure why it won't work in a Pegasos.. but the most likely issue for Efika users is that it's a 5V PCI card and the Efika needs 3.3V devices. If it's a true 3.3V card, then it may simply be designed wrong.
There are very, VERY few systems in the world that actually expose 3.3V PCI slots (except high end servers) that can take a graphics card so board designers simply don't design or test for these scenarios when there are a billion x86 PCs in the world with 5V signalling.
Back to the Pegasos, well.. maybe it's bad luck, a broken card of some other variant? It could be a symptom of a dying processor or northbridge/southbridge combination, too.. Linux seems far more "fussy" about this kind of thing than MorphOS ever was.