Hey Guys, thanks for the suggestions. No, the whammy is the only control on the Expression pedal and it replaced the Wah in my signal chain, so it's not that. (Would've been a rookie mistake :) )
I've tried building a patch from scratch with just an amp and the Whammy to rule out any weird conflict with Overdrives/Eq etc but it still changes the tone fairly drastically.
I'd be in the same boat in that it's pretty much the only effect where I feel the HD was better. I'm not sure how to get around this...