Okay, now I understand. I don't think the water is coming in under the slide in the gap you are referring to.
I had a problem with mine like you are saying...it only happened when the slide was in. In my case, since I did not drive it in rain, I discovered the issue when parked on a slight sideways tilt or driving rain on that side of the coach. After spending hours searching out the solution I finally discovered it. Here's what I did...
Put the slide out a few inches and run a garden house on the face of the slide. Be careful not to get the underside wet. Look underneath the slide. I found water dripping from screws that penetrated the membrane that encases the underside. It turns out the facia trim on the lower part of the slide was not caulked. Water would seep in and get under that membrane then leak into the coach coming out where ever it could find a break in the membrane.
It was never an issue when the slide was out because it just dripped on the ground, unnoticed by me.
Normal rains also weren't noticeable because of the way the coach is designed. There are weep cups at each end designed to hold the water wiped from the sides when retracting the slide.
Anyway, it was an easy fix. Just apply caulking to the top of the lower facia trim on the slide. I also then went around the rest of the coach and found caulking inadequate on the outside TV and the hot water heater.
I hope this fixes your problem.