Also, it's two different guitars (unless you've tried the same hardware, pickups, amp setting, speaker, effects setting, string gague, setup, etc. with the different tonewoods). Who's to say you didn't get a very warm-sounding piece of mahogany and a very bright sounding piece of ash? It's generally held that wood varies more within its own species than from species to species so while there is a difference (for example, a maple neck always has this special sound to me), it's a lot less than we usually think (blame the hypists) and probably much more felt by the player than heard anywhere else. Not to mention that a tiny turn on your amp's treble knob, or mid knob or whatever would have a bigger difference anyway.
*End most repeated rant on forum*