Mike,
That is very odd. The project settings are fine, and it makes no difference for the emulator to load little or big endian code (i.e., there are no settings for the debugger itself).
I will have to try using my XDS200 on a Hercules board tomorrow and see if I can reproduce this issue in Linux. I don't have CCSv5.4, but I will see if v5.5 works fine.
Regards,
Rafael