GPTOM, This is a tough one, at this point I would have to actually see what's going on with your loader.
Could be drive or guide wheel problems. To my way of thinking unless the micro switch is being activated it doesn't make sense that it would start it's drop sequence early. I don't know for sure, but I dont think TMCC would be a factor in this. It's pretty much electro- mechanical in regards to the picking up and dropping part.
Any chance of posting a short video of the action perhaps from the open side of the rail? I hope KD will chime in here as well...
John