I have had similar problems.
One season, I found that although I put antifreeze in the bowl when we stored the trailer for the winter, when we came to take it South in Feb., the bowl had dried out.
When we got to warmer weather and got water in the trailer, I found it would not hold water. I tried cleaning the seal area numerous times - with popsicle sticks, then with my hand, suitably protected in nitrile gloves! I didn't find any obstruction and my cleaning attempts didn't resolve the problem. The water would run away in maybe 5-10 minutes.
I even took to dropping ink into the bowl full of water in order to see which area of the seal was leaking - that did provide an indication of the area that was leaking, but I still couldn't stop it.
At this point I figured I was going to have to lift the toilet and buy a new seal.
Just as an experiment however, I applied a thin layer of silicon grease to the seal and that seemed to do the trick!
You wouldn't think the seal material would absorb water, but I have a suspicion that if it dries out it doesn't work as well.
Once I got it sealing and it held water again, I didn't have any further issues - not yet anyway - that was a couple of seasons ago, and it has even been fine again during winter storage with antifreeze. Never have put any more silicon grease on the seal.
Brian & Connie Mitchell
2005 Classic 30'
Hensley Arrow / Centramatics
2008 GMC Sierra SLT 2500HD,4x4,Crew Cab, Diesel, Leer cap.