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Can this problem be worked around? I guess this happens because Pegasos says something into serial port, unexpectedly gets it back and crashes. Is there a way to disable that failing test on the serial port ?
No...
Unfortunately the serial port is used for early debug and as a failsafe if anything dies like PS/2 keyboard/mouse or display. The system requires some kind of input/output console to be present for user intervention (even if it is on serial and simply not connected, and the system is set to autoboot, the serial port has to be there).
If you're looking to do something like this you'd probably need to get the Pegasos or Efika with a custom firmware which did not attempt to use the serial port in the way it's using it, however this begs the question of how you control the system if the serial port is not used. Can you rely on graphics etc?
Developing the project for Efika, would probably be better done if you used the internal IrDA connector attached to PSC6 - it has the 3 data pins you need (actually you will maybe need to drive it manually using GPIO and mimic DTR) plus ground. It is not RS232 but you are making your own circuit so this doesn't really matter.
For the Pegasos.. I am not sure how you would want to prototype it in this instance. You may be able to configure the VT8231 to support the IrDA pins in the front panel header to act as a serial port (check the VT8231 docs they're off Google) and see if you can drive it. At least then you get a 1-wire interface that can be connected to a 3-wire serial port header with the same pin format on both devices..