[This answer works for me using Qt Creator 2.0.93 (beta 2.1), YMMV]
I spent some time fixing a similar problem: using a non-intermediate, unsupported build chain from Qt. It seems that Qt Creator uses different environments for the build steps, based on whether you use the "Make" or "Custom" step (see the "Projects" view). The only way I could control the actual make invoked and, more importantly, the path from which it was launched, was to go from using the "make" steps to the "custom" build step. As soon as I did this, the settings for the PATH environment variable (in the build environment) were completed and the correct make was chosen.
In other words, try the following:
- Set the path in your build environment so that the project includes your cygwin stuff.
- Create a βcustomβ build step that invokes Cygwin with the appropriate parameters (copied from the old build step).
- Remove the old build step.
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