Any other version of AE on the system? If so, the relevant MPEG CoDecs might be tied to that version and CS5.5 incorrectly resort to those. short of deactivating the other version and reinstalling CS5.5 once more I can't see a way to fix this...
I do currently have AE CS4 installed on my machine and it imports and runs m2ts files fine.
I may try uninstalling my current version and reinstalling CS5.5 but man that sounds like a nightmare.