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I wonder if your last point may be key, and I want to test that in a minute. I forgot one thing that changed around the right time to be suspicious.
To use the tf1260 ide you need to have the ehide driver loaded either via loadmodule off the motherboard ide or by being burned into a rom.
Although almost everything does seem to work fine I did switch to custom roms around that point. These were 3.2 roms purely with the ehide driver loaded as well.
The working card is not 3.2 based and so did need tweaking to load off my 3.2 roms anyway (workbench and icon library) If the rom is to blame that would explain why the bad cards seem to work OK under winuae which is off a clean 3.2 rom image.
Will swap out the custom roms in a minute after running a hddreport on the bad card.
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