You need to MEASURE the distance between the bottom edge of the top half and the supports that the top sits on when it is lowered). If one side seals properly, use that measurement as the "goal" value. If the other side is lower, there will be a gap.
You can see the sealing gaskets at the door opening. There is a gasket on the top half and one on the bottom section as I recall. Or perhaps there is just one gasket that rises to the level of a "lip" or something similar on the other half. They should meet. If they do, that is a height to shoot for.
But, it is entirely possible you are missing a gasket. You may be able to check for this on the outside using a mirror with the top up. You should be able to see the gaskets on the side that seals. If one is missing on the other side, it should be obvious.
There's been a post in this forum about replacing gaskets, if that's your problem.
Edit: Here's one of the posts about replacing the gasket: http://www.hilotrailerforum.com/f55/...of-gasket-220/
Looks to be a big job. Make sure that's your problem before you start.