With my passport, that has the cables as well, I usually bring the slide all the way in, essentially until the motor stops. Basically once in, I usually give it a couple extra clicks. You can tell its all the way in because the motor pretty much doesn't turn anymore and the slide doesn't jerk anymore.
Maybe this isn't the proper way to do it, but from listening and seeing the action I don't feel like the motor is really "straining" or anything, just that its reached the end of travel.
What I would do is make sure the carpet is dry and pull the slide in until you feel that it is all the way in. At that point you could wait for the weather or hose it down. I would also check prior to this that all the seals and "flaps" are facing the way they should be and or are not damaged.
It is my opinion that when you said "seems like the right side of the slide seals completely up against the seals and the left side isn't as tight but appears to be touching the seals. If I keep pushing the button down, the left side will get even tighter.", that you are not pulling it all the way in.
Either that, or it is slightly out of adjustment on that side or your on unlevel ground contributing to the alignment issue. If it is truly an alignment thing I would take it to the dealer.