On both MX6s that I have had, I always have to "give it a hand" when it is closing. When it slides forward to close, then it stops going forward, and lifts upwards to make the seal. Every MX6 I've been in (4 so far)--I'm talking 1st Gens of course, has this problem. I don't worry about it, I just keep holding the button and give it a gentle push UP when it starts moving up. Otherwise, it will not close all the way.
I don't know if that is your problem, but you might give it a try before you go spending more money.
Just make sure your weather stripping looks good. You probably need to clean it since it has been leaking, that may help also.