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peeknamedpipe stdio error

I'm having a problem with a windows utility that I have written. It uses
the windows API function peeknamedpipe, readfile and writefile to connect
to a console program that has been compiled with gcc.
The program reads the stderr, stdout and writes to the stdin using these
This method worked perfectly well until a more recent version of cygwin.dll
has been installed.
Peeknamedpipe will not return that any data has been written until the buffer
is full, this causes problems with writing to stdin. This happened with stderr
before (which wasn't a problem for my program) but now seems to affect stdout.
Another thing I've noticed is that end of lines are now just linefeeds and
not carriage return followed by linefeeds as before.

I think this problem could possibly be due to with how the program I'm connecting
to has been compiled. Maybe it's not flushing the buffers after writing to
them? Unfortunately the programs are created by an automated UML modelling
tool and so my control over the content is limited.

Any help would be appreciated.


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