Reinier:
I saw a similar situation when I moved from CCS 3.2 to CCS 5.5 - here is my post:
http://e2e.ti.com/support/development_tools/code_composer_studio/f/81/p/308044/1073185.aspx#1073185
I was surprised that switching to a different level of code gen tools and back fixed my problem, but it might be worth a try for you...