First off, make sure your tt is level.
Did you have high winds with the rain?
The reason I ask, I had a similar problem with mine. I was a little street side and nose high and we did have some high winds with the rain. It left just a little water in the floor by the slide. Because of the wind rain was getting in under the slide.
I checked all seals as you did and everything was good. I have since camped in the rain with some high winds, but I made sure the tt was level and it hasn't leaked.
Not sure if this will solve your problem, but it's worth checking into.
Good luck and let us know how things turn out.
Gary & Trish
"PT Crew Member Since 11/2010"
2017 Prime Time Crusader 315RST TE 6.0 : 2007 Flagstaff 206ST MAC Series
2012 F-250 Lariat : FX4 : CC : SB : 6.7L Diesel : 3/55 Gears
2016 Nights Camped - 9