+4  A: 

Yours is a frequest source of complaints regarding mixing eclipse & cygwin. The crux of the problem is that eclipse understands only the windows environment & cygwin, well not so much.

Define your paths in in eclipse windows style. Also is /usr is under C:\cygwin, you have to give it the full path. Otherwise eclipse is going to try to find it under c:\usr and come up empty.

Also, are your path definitions appending to or replacing your windows environment? You'll probably be happier appending to your environment rather than replacing.

Never tried autodetect - you may have to hard code those paths in .cproject

DaveParillo
Thanks, I managed to fix the warnings by turning off the automatic discovery and manually adding the paths *'Windows style'*. Too bad it doesnt work with Cygwin out of the box like NetBeans does.
Amro