This is killing me and Im sure its simple - if im in step record and I press say a c4 when the sequencer coms around again the note is right but the LED isnt a C4? I hope Im making sense. Im not a keyboard player so Im relying on that feedback for a number of reasons

Do you have a transposition going by any chance? Press and hold the transposition button and see if it says anything.

I had the same problem just today and it drove me nuts for a while until i realised there’s an active transposition.