The shifting letters in the title sequence are a nod to the fact that Monk has OCD, and therefore likes things to be straight.
I just solved the case.
Monk often undertakes actions which would result in evidence and investigation being compromised. Since he is no longer a police officer, these actions could result in cases being dropped or overturned upon appeal. There is no way that the San Francisco District Attorney would allow Monk to perform the actions that he does.