Have a similar problem and determining the actual problem is tricky.
Sounds like you are on the right track.
In my case, it appears that a piece of plastic on the bottom side of the slide, which acts as a "drip line", is actually routing water into the trailer. When it was raining I went out and could actually see water dripping from the end of it onto the trailer floor.
Your issue sounds similar. I'm going to remove the "drip line", inspect everything, and hopefully just reacaulking it will fix it.
By the way, my trailer is still under warranty, but I would much rather do the repairs myself if possible. Especially issues like this which can be tricky to diagnose and correct.
