Confirmed that the gasket isn't being compressed properly, snapped a pic. The left side shows good compression, the gasket bulging in to fill the opening, but the back side isn't showing much compression at all.
The center seam for the roof also looks like it might be an issue, the way it is bulging doesn't look like it would seal properly without some help.
After some work, I was able to remove the unit to get at the roof, apparently the original install wasn't centered properly, and the hole could have been slightly larger. Now I just need to figure out how best to fix things up.