The max transfer affects large file transfers and writes, this is what I have figured out anyway and might not be 100 percent accurate. So if the app is doing lots of large file operations it might cause it spaz out. I am sure this is down to a bug somewhere in the controller that affects newer drives. This bug never materialised when doing single file transfers though.
When transferring stuff within winuae to the cf I had no probs. once the cf hit the Amiga that's when the bugs hit. Hence the need to set the max transfer to avoid issues.