soft spot not getting bigger, concern?

Wow, this may sound really stupid but ....I know we had water in our front hatch after heavy rains and we also had some water along the wall inside by the door. Camping World (where we bought the trailer new in 2012, a Winnebago 30RE) repaired the wall that was showing slight "bubbles", what they actually did was put a new wall over the old one. They said it was fixed, yea.....well, we continued finding water in the front hatch, checked on the roof and found some small pin holes in the caulking around the TV antenna, and along the seam in the front. Replaced all of the caulking, every thing is dry but now there are some small soft spots on the floor. They have not got any bigger over the past summer. We keep the trailer stored outside beside our house. We pulled up the vinyl floor in the hatch and it was put on top of 1/4" plywood, I'm assuming (Yea, I know) the floor is that way through out. We pulled one of the heat vents on the floor but could not tell if the floor was the same since they are "ducted". I really don't want to pull up the vinyl if I don't have to but... I hope this makes some sense. Thanks!!!