I had 5.00 M33 for like a day and I had the same problem.

Game starts up and the message flashes up at the top about pressing + & -.
NitePR screen comes up and I press start.
Code screen comes up and I select the codes I want but it's like they never work in the game. To me sounds like the same problem.

What I ended up doing is going back to 4.01 M33-2 (or M33-3 whatever is newest one, not sure if there is a M33-3 for 4.01)
I still use NitePR rev K though and you MAY have to re-install the NitePR.
On rev.K did you choose the file that says "for all other CFW's"?

Maybe if you hear of anyone else using NitePR with 5.00 M33 you can ask them (by sending a PM) how they got it to work and then post the answer here on the forums cuz I know others are prolly having this happen too.