I am posting this with the hopes that someone here has an answer.
I originally bought GPO as a member of a team of musicians in different locations in the U.S. who needed to all use the same orch sample library for continuity. GPO really fit the bill. We were not writing, but transcribing. So, I never ran into this pproblem (tracks already existed with correct mod wheel info) until I tried to use GPO for composing.
I am having the following problem. I have used Logic for about 7 years, very familiar with it. I have unchecked every box possible, and I am still getting reset mod wheel every time I press stop/play.
Unfortunately, for now, I have stopped using GPO. Very frustrating indeed.
[Mac Pro 2.66quad / 1G ram / Logic 7.2.3 / Mac OS X.4.9]
-shows that it is supposed to be fixed in version 7. (more details at the link.)
I'm still on version 5 so my work around is to hyperdraw in the arrange window some mod wheel changes just before the start of where I want to record. (Make sure your track is set as "read"- not sure if this is still there for v7).