I had a similar bug yesterday, on my Tuscan RM, i went into tuning to see what modifications had been done, and Stage 2 and 3 engine upgrades weren't installed. I cant remember if I had installed them before, but it said it had stage 1 installed so im guessing I obviously forgot to install 2&3, or possibly theyve been deleted somehow. So i went to install Stage 2 and it said I had to install parts in order, but I had stage 1 installed already. I went back to the home screen and started again, but same problem. I even tried to install it from my items list, in case it was a fault with the tuning shop itself, but it wouldnt let me install it.
Anybody had a similar issue?
I wonder if its RM related, as the OP was also using an RM, albeit a different car though.