Unless you're running your platform pedals with SPD's, it could well be your shoes compressing. IMHO square taper is noticeably less stiff than any of the shimano hollow axle designs. If you're switching from a bike with a stiffer setup you will notice it.
I've always been of the opinion that Ti SQTP axles are a bit silly because the shaft diameter is limited in size by the bearings, thus you can't make a bigger diameter Ti tube BB axle that is lighter and as stiff as it's steel equivalent.
I've had to downgrade to SQTP on one of my bikes because I can't find an M950 middle ring, but on my bouncy Marin I'd never be able to tell the difference.
Oh and I've heard terrible things about ISIS from my best mate.