http://sources.redhat.com/ml/cygwin/2003-03/msg01529.html
There is obviously an input buffer, which overflows if you keep an open filedesc. on a serial port and let some external system generate input data on that port while your own app does not read them away from there fast enough. The message referenced above (from March 2003) also contains a reliable way to reproduce this problem. My guess is, that the tcflush() itself is probably not guilty in any way, it just helps reproducing the problem.
;Henning
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