Thanks for the suggestions!
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Did optimize the bios setting for speed and the problem was back.
In my case (if i remember correctly) it was a setting that clocked the ISA bus higher than the 8MHz.
Also there was something with IO recovery time.
Have to take a look at the bios to see what the exact options where.
Currently the TB card is in a 486SX25 industrial system, there are very few options to optimise the BIOS and I disabled allready the BIOS shadow function. There is the option to set system start up speed to "low" which is kind of an internal turbo button. So I did this (meaning the whole machine is running with 8MHz) but the only effect was a really slow 486 PC and the same error message appearing some seconds later.
How does the card look physically? Are there any visibly bent leads or damaged traces?.
If you feel up to removing and reinserting the chip, you can use something flat, like a blade, to bend one row of pins (or both) slightly outward, for a better connection.
There are some leads at the emu that are a little bit "uneven" I would say, but nothing looks really damaged. (Maybe I can post a picture)
Removing and reinserting the chip seems to be an interesting but also somehow final option.
Are you sure this chips is controlling the Proteus operation?