Sludge,
I was thinking about the brakes system in FSX and tried to do some research. From what I understand, if you have a single button mapped to brakes, it will apply 100% brakes, whereas if you use pedals you can have more dynamic braking similar to RL. Not sure why FSX would only read it sometimes, but perhaps it has something to do with that.
That also led me to the idea of using the PUSHBACK command instead of brakes. For example, when the hook is down, and you trap, the pushback function is automatically engaged until you raise the hook. It would prevent both the rolling forward in MIL/MAX, and allow a bit of roll back...two birds with one stone. Of course the obvious flaw with that idea is that you would roll all the way off the back of the boat if you didn't raise the hook. I was just thinking that perhaps it could work since pushback is simply an on or off command, whereas there are varying amounts of brake percentage.
If you post that XML for the trap brakes I'll mess around with it. I really only know C languages and VeriLog, but I'm sure I could figure it out if I dedicated the time to it.
Pyro