Latest updates delete System/Library/StartupItems folder

One of the following updates delete the System/Library/StartupItems folder:
Migration Assistant Update for Mac OS X Snow LEopard 1.0
Remote Desktop Client Update 3.5.1
Safari 5.1
Thunderbolt Firmware Update 1.0
iTunes 10.4
iWork Update 6 9.1
This is on a MBP 13-inch, Early 2011 running 10.6.8.
It causes the machine to freeze at intermitent periods of times and reports the following error message in the console:
com.apple.launchd [1] (com.apple.SystemStarter) Failed to count the number of files in "/System/Library/StartupItems" : No such file or directory
There have been posts on how to fix this, but why is it being deleted by these updates?

I have the same console mesages repeating ad-nasium as you do. What is interesting is I do have the StartuoItems directory but it is empty. The problem I have is that the log-in window comes up as normal, but I can not type in it for about 5-8 seconds. This has started after the latest updates which you mention. Don't know if this issue is related or not. Have deleted the loginwindows and loginitems preferences to no effect.

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    Mar 20 11:24:12 mac /System/Library/CoreServices/backupd[19136]: Deleted backup /Volumes/Time Machine/Backups.backupdb/mac/2008-03-19-101713: 50.19 GB now available
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