Have you tried setting an RPM limit? According to the MoTeC software, over RPM is for when the engine exceeds the diagnostic RPM limit. It could be as simple as 5000 or whatever the engine is running at, is greater than 0.
As far as not being able to go above 5500RPM, what does it do at this stage? Backfiring, becoming "sluggish" and not wanting to go above this RPM? Do you happen to have a log of the engine running and running into these issues?
Cheers,