We use Butyl caulk for sealing the end of the side hatch-gaskets near the hinge. We squirt a little into the end, and put a small blob on the end. When you push it on, push it tight to the hinge. Clean off some of the excess, but you need to leave a little behind for sealing. Make sure the caulk doesn't block the rain gutter area.
Sometimes you need to tighten the fit along the entire length. To do that, remove the entire gasket and pinch the gasket along the area that slides on to the aluminum rain gutter. Then re-install the gasket. The gasket should not need sealing along it's entire length.
To test the gasket and seal, OPEN the hatch and run a small stream of water onto the roof above the hinge. Increase the flow until it ALMOST starts to over-flow the gasket by the end of the hinge. It shouldn't leak unless the water over-flows the top of the gasket.
If it passes the "open test", close the hatch and test it closed. Again run a stream of water above the hinge so that it runs into the end of the hinge you are testing.
Before opening the hatch, shut off the water and let the water drain off for a couple minutes. If you open it too quickly, you may get a false leak from water that sneaks in when you open the hatch.
If it passes the test, close the hatch and try again with a spray pattern simulating a heavy rain. Don't blast the gasket directly with a strong stream. Normal driving and rain conditions will not create a blasting stream, so that is an unrealistic test. A good seal may still leak a little if you are washing the trailer with a pressure washer or spraying directly into the door or hatch sides. When we test, we spray water at the seal areas holding the sprayer about 2 feet away and spraying at about a 45 degree angle to the hatch or door. We spray from several different directions. (this simulates a strong blowing rain or rain while driving)
IF the hatch still leaks when closed, after re-sealing the gasket ends:
We have changed the way that we finish the hinge area of the hatch. I will try to post a few pictures showing the before and after of the modified area. Making the modification on older units that have developed a leak will usually fix the leak. If customers stop by the shop with their trailer, we will do the modification for them. Otherwise, I will create a set of instructions in case you want to try the modification yourself.
The modification takes a little time and patience but only requires a small file, so it should be within the ability of most people.