My problem is similar. I just upgraded from the 4S to the 5 and I used to be able to sync the calendar on my iMac and iPhone using iCloud without getting duplicates by selecting/deselecting the appropriate calendars on the respective devices. Everything synced as I entered it.
I'm pretty sure it was working with the 5 until recently...
Today I noticed that an event I entered on the 5 for last week didn't show up on my iMac. When I checked the EDIT screen on the phone to see what calendars were checked, only the calendar for that event was (on the All on my iPhone). All but the Unfiled calendar are checked on the All on my iCloud. When I unchecked and rechecked the calendars under the Phone didn't help. Can't get the thing to sync...
Seems like most people are having problems with Exchange accts, but here I am with my iMac/Phone/Cloud...