I and many others have the same issue. As far as I can see there is no permanent fix. The best one can do is a battery pull and plug the phone in while it is rebooting. It should then charge as normal.
If anyone does have a fix I would love to hear it.
This only happened after I did the OS upgrade two weeks ago. When plugged into the wall charger it says "This device is unable to charge your Blackberry" and then goes on to say that some USB ports don't have enough juice, etc.