Regarding your first problem - sounds like some sands are in the works of the Global Scheduler, but we'd need to look at log-files and a few other things.
Regarding your second problem - never heard of that / seen that. You may want to check your CONSOLE.EXE.LOG ... I would suspect that this should be duplicable with a backup of your DB, so you may want to prepare that before you raise a support call.
Also including the SP5-install log as well as the COREDBUTIL.EXE.LOG from the Core might give useful insights in what has/has not happened.