We've got two Macs that are both running 10.6.6. On my MBP, Adobe (Acrobat) Reader started behaving weird a few weeks ago. It became very sluggish, started missing mouse clicks or mouse button releases, scrolling was next to impossible. Most of the time it does not handle Page Up / Page Down events at all. Zooming works erratically if at all. It's basically unusable. On the other Mac (an iMac), there are no such problems. I've tried to remove and reinstall Adobe Reader as well as upgrading to the latest version, but unfortunately without success. This is the only software that is behaving strangely on this Mac, everything else is working fine. What else could I try?
Do you have RightZoom installed? Create an exclusion for Adobe Reader in RightZoom (Cmd+click RightZoom app).
I hope this solves your problem; I just solved this on my own system today.
(If you don't have RightZoom installed, open up a guest account and log into that and see if Reader is slow there. I assume it is some incompatibility between Reader and another app or setting hack.)