Greetings Riley,
When iCal is talking to a server (the updating you see at the top) it is pushing changes from the computer to the server and back down again. If you quit the program before the push is complete, iCal will re-open itself in order to complete the push so the changes are not lost.
If you are confident you have waited several seconds after the updating badge does away then there may be a cache or preference that is not working as it should.
Troubleshooting:
1. First make an iCal backup: Click on each calendar on the left hand side of iCal one at a time highlighting it's name and then going to File Export > Export and saving the resulting calendar file to a logical location for safekeeping.
2. Go to iCal > Quit iCal
3. Remove the following to the trash and restart your computer:
Home > Library > Caches > com.apple.ical
Home > Library > Calendars > Calendar Cache, Cache, Cache 1, 2, 3, etc. (Do not remove Sync Cache or Theme Cache if present)
--- NOTE: To get to "Home > Library" in Lion: Click anywhere on the desktop and then click on the "Go" menu at the top of the computer screen while holding down the "option" key on the keyboard. You will see "Library" in the menu.
4. Launch iCal and test.
If the issue persists:
1. Go to iCal > Quit iCal
2. Remove the following to the trash and restart your computer:
Home > Library > Caches > com.apple.ical
Home > Library > Calendars > Calendar Cache, Cache, Cache 1, 2, 3, etc. (Do not remove Sync Cache or Theme Cache if present)
Home > Library > Preferences > com.apple.ical (There may be more than one of these. Remove them all.)
--- NOTE: Removing these files may remove any shared (CalDAV) calendars you may have access to. You will have to re-add those calendars to iCal > Preferences > Accounts.
3. Launch iCal and test.
Hope that helps!