Winnebago's have single piece fiberglass roofs, and there is a seam that is stuffed into the gutter channel as you know. If it's in good condition, I'd check the front and rear end caps seams. If water is getting in that way, it can travel quite far before staining the ceiling. Note that a puncture or crack in the fiberglass might be in play as well. And of course, nearby items that needed holes in the roof could be suspects so check the caulking around them.
Here's how it's made...Journey's have the extra foam insulation installed, lower end models it's not:
I used Eternabond tape for both my end caps.