Finally figured this out after digging around the registery. It appears that with my current wsx file it isn't registering the full path to the executable including ".exe" at the end. This is what is causing the config file name to be confused. Why in the world this makes a difference is beyond me, but just another thing to annoy me about windows i guess...
To fix, changing the Name on the File element in the segment above to be $(var.XXX.YYYYYYY.TargetName).exe instead of just $(var.XXX.YYYYYYY.TargetName) seems to work.