If you think that the bed end leaks past the upper rubber seal, have you tried tightening the Roto-Vise handles slightly? You do not want to crush the rubber seal, just enough so that a dollar bill between the door and the seal will not easily release when pulled. There are several posts on here that explain how to tighten those handles.
Also make sure that the bunk end top rubber seal extends a bit past the vertical seal on each end so that water sheds off the end and not onto the vertical seal where it can enter the tent area. Also make sure you zip your windows closed, as any leakage is usually trapped on the vinyl tent and not leak into the inside bunk end.
Another thing that I do is to purchase some of that BLUE painters tape 2 to 3 inches wide. I put a piece of that tape over the gap from the bunk door edge to the camper shell covering the gap. The tape is water proof so rain will shed off the tape. Because it is painter tape it should release easily in the spring. Purchase a name-brand tape if you do this.
Finally I also use some tape and cover the rear clearance light seals above the bunk door just in case the seal around the lens allows water to enter the bunk end closer to the roof. I eventually used Eternabond white tape to do this is lasts year after year.
You might want to store the trailer on a left to right side slant to promote water and snow running off instead of sitting on the top. I would NOT use a cover if it was me. Many reasons for this. I would make sure the roof is sealed with Eternabond tape... only need a 60-70 degree day with enough sunlite to see and maybe 4 hours to get this done.
I have made a posting of using Eternabond tape to permanently cover the Dicor and close gaps on the roof and have it last for years. This was done in 2015 and having just inspected my roof last week, it still looks new, like it was installed last month. The post is here...
https://www.forestriverforums.com/fo...nce-90060.html