Most of the time when you don't receive any responses is because others are not having the issue you are having or there isn't enough information for anyone to even to start to help. I will say that we have thousands upon thousands of machine running Mach4 and cutter compensation without issue, so you are definitely not the only one using cutter compensation. And don't take this the wrong way, as I'm not telling you that you are "not having a problem". I'm simply stating that there is something unique that is happening that we have to solve. With that in mind, the rest is dedicated to that end.
1. We use Fanuc type C cutter comp. The rules for cutter comp entry and exit are given Chapter 4 of the Mill G Code Programming manual and I believe them to be correct.
2. Have you tried a later build? I don't remember any cutter comp issues with 4612, but that doesn't mean something isn't amiss with that build specifically.
3. What other machine operate to your expectations? Could it be they use a different style of cutter compensation?
Most G code includes a safe start line similar to "G40 G80 G90" to put the machine into a known state. if you stop the machine when in cutter comp mode, the machine is still in G41/G42. Simply entering something in MDI does not magically clear that. The reset button should be used to put the machine into a know state. Look at any Fanuc control and you will see that the reset button is the most worn button on the machine!
Anyway, if you stop the machine when in cutter comp mode, the machine is still in G41/G42 unless you do something to change it (reset, MDI G40, etc..).
Also, please provide the G code program that you are trying to use, as it is impossible for me or anyone else to guess why you are getting the results you are getting. Someone may spot an issue right away. Otherwise, create a ticket with support and give them the G code file and tell them the results you expect.
Steve