In addition to enhancing XProtect, the Security Update 2011-003 will also scan the Mac’s entire drive, looking for and removing any previously installed Trojans. This one time scanning process should take less than 5 minutes after installing the security update and rebooting, and the user will be informed if anything was removed.
In rare cases, it has been reported that this scanning process hangs, therefore causing the Mac to run slow. When this occurs, a process named MRT will show in the Activity Monitor consuming a lot of CPU activity. Rebooting the Mac will not cure this issue, as the MRT (Malware Removal Tool) process will start up again, trying to complete it’s one time scan. The confirmed fix for this problem is to run AppleJack (it can be caused by damaged directories, messed up permissions, or corrupt cache files).