That happened to me with March 2013 updates. The machine was stuck with "Operations are in progress" -message for 12 hours. At that point I deduced that it is unlikely for the machine to actually be doing anything.
The real question is: What to do?
Force the thing into reboot cycle?
Wait a while longer?
I chose 1. and was ready for the smelly thing to hit the fan. Nothing happened. Windows finalized the updates during boot, which is pretty much normal in the circumstances. After that I logged in and everything worked fine.