Thought about it for a little while, then realised I still had a working v5.4 install for the same projects on another PC, so opened up the project compiler and linker settings and made sure they were the same in the v5.5 install.
there were a few things missing from the settings in the 5.5 project, and not anything I would have got anytime soon, if I remember correctly it was to add:
"${CG_TOOL_ROOT}/lib"
"${CG_TOOL_ROOT}/include"
"${PROJECT_ROOT}"
to the C2000 linker library file search path.