If IE is in the Unapproved Applications list (btw, you can see this in the Client GUI as well, see View Logs > Client Management/View Logs > Control Log), then its MD5 hash is not in the whitelist.
Perhaps the IE was updated in the meantime, that's not unusual. But if you are absolutely sure that IE was not updated, you should be very careful to overrule System Lockdown. If you do it, you should be sure that iexplore.exe is not malware (scan it or let it check by virustotal.com).
In my opinion, whitelisting via System Lockdown is a feature for very special environments. It's not intended for the typical Windows box with its frequent patches.