I noticed that if I placed a configuration variable in both the UCF and the PCF, then the UCF was "cancelling" the PCF. In both files, I was using the ">" sign to append the definition.
For example, I had MS_MACRO defined in both, using the ">". The result from the UCF showed up during checking, but not the PCF. If I commented out the UCF definition, then the PCF result would show up during checking.
Has anyone run into this before?