The only thing I can think of would be that another mod has modified your controls somewhat. One mod in particular that I can think of is "Sharing and Caring Companions", which maps a certain button to some function I can't remember at the start. Try going back a few saves until you notice that the problem isn't there. Then, you can find out what you did between that point and the next save that might have messed with things.
Of course, you might also just have added a mod that conflicted with something, causing the aforementioned control issues. Does the problem persist with all mods disabled?