I had strange problems with the alarm clock after flashing the leaked MR2 update from June 10. They cleared up after clearing the data from the "Clock" app (Menu, Settings, Applications, Manage Applications, Running. Go into app and use the "Clear data" option).
I've experienced these types of issues numerous times with various apps after updating via an OTA or flashing a full RUU. That's why I always do a master reset (factory data reset) now to clear the slate and nip them in the bud! It always does the trick.