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Check Windows...
Whatever Windows shows the com port and IRQ as is what the BIOS sees it as. Compare Windows com/IRQ settings to your Linux IRQ settings.
setserial by itself will show you the IRQ and UART settings for a com port.
setserial /dev/ttys2
...will give you IRQ and UART info for that port, for instance. If the two don't match (Linux and Windows), you need to change one or the other, either modem or IRQ for that device.
Xayd
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