-One side has a BumpStop and the other doesn't.
-Someone before you swapped out lower fork assembly because of a accident.
-The Shock isn't sitting in the Lower Fork assembly the right way.
-There is a Rubber bushing that is missing in the Tophat or there are two on one TopHat and wasn't realized
-The Shock's tophat isn't meeting up completely with the inner Strut Tower housing
-Blown Shock like "My Honda Is Slow" stated.
-One shock isn't the same as the other and doesn't compress all the way down


Those are just a few things I could think of, I've seen this happen before and one of those examples I gave above ended up being the problem.

G/L and keep us posted on the problem/solution.