I believe I do it the same way every time, which is to be on the episode that the guide says is currently playing and then press the "OK/Select" button on my remote, and the episode starts playing "in progress" (when it's working correctly, of course). The thin purple line under the episode is typically correct in terms of how far into the episode it starts to play, percentage-wise.
I've gone for long periods with the guide data being fine, and then this problem crops up "for a while" and then settles down. I'm throwing darts at the wall here -- but I wonder if these issues crop-up after making changes (adding or deleting shows from a virtual channel). I tend run these channels for months at times with no changes, and then I get in the mood to switch things up.
EDIT: And, I did add/delete some shows from some of my virtual channels earlier this week. Maybe unrelated, but just wanted to let you know.