I suspect the rolling resistance is the main difference both tires and aero position but mostly the tires. I had a mtn bike that I put a really good quality tire of the type you have slick in the middle and tread knobs to the side and when I later replaced it with a true slick it was a lot different. The one bike could just be freer rolling also. The test would be take them both to a hill and coast out till you stop. Mark where you stop on each bike should tell you.

Geometry could also play a part. Line the two bikes up side by side and take a photo straight on (from side). If you are doing your hills seated on both bikes look at bar position and seat to centerline of crank for a clue.