This sounds REALLY strange! I take it that you first press SHIFT, then do the drag?
Still, fact is, if the group node resizes instead of letting the node pass, there is no SHIFT-key-down recognized. And, feature is working here as expected and described.
Since I wouldn't assume that a computer's SHIFT key *consistently and always* fails at exactly and only this operation, one other possibility would be that for some reason, your yEd installation got corrupted.
This is not entirely impossible, after all.
With that in mind, you may wish to download a fresh copy of yEd and install that.