Hi David,
Can you provide more details about your project? Does it use SYS/BIOS?
Also, there were a few bug fixes made to command-line builds in CCSv5.5 if you are willing to update your CCS version. It may address your particular issue (don't know for sure). Unfortunately I think incremental updates are disabled for CCSv5.5 so you may have to do a whole new install which I know is a pain. One thing I can say is that CCSv5.5 is pretty much the last of the CCS updates for v5 so once you get to CCSv5.5, there will not be any more patches for it (there will be no v5.6)
ki