Folks,
This is actually a bug in the 14.3 core generator tool. I've determined this by going into the tmp directory the tool produces when generating the core and found that the tool is using relative paths for files called out in a .prj file (that is generates on the fly) for the core when run from my C drive. Once I use my source control directory with a mapped drive the tool starts using absolute paths that are pointing to the wrong directory! Looks to me like the script writer screwed up the path extraction in 14.3, which used to work in 14.2.
It's unlikely anyone else would run into this kind of problem, but I figure I might as well document the issue in case someone else runs into this problem. Until Xilinx fixes this the only solution is to run it in a local temporary location, then copy the results back to the source controlled location.
-alan