Not sure what seals you are talking about or the situation described. The real seals are on faces of the inside frame around the slide and press against the side wall to seal. They should seal all the way around. There is often a D-seal at the edge facing in toward the slide as well; those help keep the water from penetrating. Those visible rubber flappers are basically wipers and rain gutters to help divert water flow, but don't actually "seal" anything. The slide topper has nothing to do with keeping water out - water blows underneath the topped in any sort of wind, so the slide seals still have to do the job.
What sometimes happens is that one of the D-shaped rubbers comes loose or gets twisted enough to leave a gap. It's also fairly common for the outer flappers and seals to get worn or out of place and lets streams of water puddle in close, where they can seep along the floor. Especially if the RV is slightly off-level and tilted so the water lies against the seals.
Some pictures of what you are seeing would help.
