Can we see your script? Maybe there's a bug in the script, or maybe the fix to get ical_synchronize to work has some flaws. Either way, it'd probably be easier to track down if we can see what you use to cause it. My attempts to reproduce the problem with the following script were unsuccessful. It just did a regular sync (not iCal) and quit.
Code:
tell application "omnifocus"
synchronize
quit
end tell
What are you trying to accomplish with the script? I know that OmniFocus will now do a sync automatically if you have unsynced changes when you do the quit command.