Winterboard works fine on 4.3.1 -- but yes, it does take a little time for some apps to update to be compatible with a new iOS. However with 4.3.1 and this latest jailbreak I have found most of my favorite apps either work fine or were updated almost immediately.
You need to provide more details if you want help. Also there is a thread with users reporting what apps broke with 4.3.1 -- and the list is pretty small so far (which is good!)
You may need to redo your JB, most if not all my apps including Winterbkard are working fine. Yes we do need more info to help you out though. If you want to see what JB can allow take a look in the Post your lockscreen thread.