You are viewing it in the layer viewer, most likely, not the comp viewer...
I wish that was it, but whether I'm looking at the "Composition: My Comp" tab in viewer or "Layer: My Comp" tab, the same issue actually happens. I've tried letting it play through once, I've clicked every setting I can think of, but still with the same result: As soon as I apply and effect, even though the clip has a starting point of 10 seconds in, when I press Play, it starts at the beginning of the clip rather than the edit point.
Even if I click the "fx" switch on and off, the moment I click the switch to "Off", the clip jumps to the 10-second start point. As soon as I click the "fx" switch to "On" the Comp view instanty switches, with the Hue applied, to the very beginning of the clip.
I can post a short video if that will help viusualize what's happening in case I'm not explaining it clearly enough.
Anything going on with temporal effects like Echo? Time remapping/ Time stretching enabled? If not, the behavior could indicate a problem with OpenGL accelerated effects processing and your card not being up to snuff, so try and turn off OpenGL in the prefs.
Duh! - I knew it had to be something simple. After turning off all Open GL options and the problem didn't go away, I re-checked, yet again, my "Effect Controls" panel, and sure enough...there was a "Timewarp 2" instance that hadn't been deleted, and the speed was at 20.
Proof again that sometimes it just take a little different perspective to see the obvious.