What did you do to center the actions screws when you bedded the rifle?
On my Wbys I always wrap the forward action screw (well, actually I use a long bolt with the head cut off) with as much blue masking tape as I can yet still get it to fit into its proper hole. I'll then wrap the rear stud (i.e. cutoff bolt) with enough that it helps center it yet I can still pull the action in and out of the stock. I usually find that the rear screw won't quite be centered fore and aft doing this but I'm not so worried. The forward action screw is more important.
All of this is done with the barrel taped, usually placing the tape as far forward as feasible. In doing this the barrel and forward action screw are in line with the forearm of the stock - assuming the stock isn't crooked. Note that it may be.
Doing it in this manner I've not had a problem.
Check to be sure you're not having any binding of the action as you pull it in and out, or that there is nothing obvious pushing it one way or another and making the barrel move to one side. If not, there may have just been some misalignment when you bedded it which shows up now.