David,
the values you are seeing for origSizes[] are default values, and the problem seems to be that they are not changed. It's a bug in SYS/BIOS. The good news is that the values you specified in your config script are the ones that SYS/BIOS will use to initialize cache, and also values that you used in your platforms are the ones that are used in the linker command file. You can verify this second point by looking into the map file after a successful build. The bad news is that to fix the bogus warning will require a new SYS/BIOS release, and there is no a simple workaround.
Edit:
David, I understand you can't switch to CCS 6, but for the benefit of other users that may end up with the same bogus warning, I need to mention that switching to CCS 6 and applying the pach as described in this thread: http://e2e.ti.com/support/embedded/tirtos/f/355/t/338321.aspx will fix this warning.