I've had a few cases where every now and then I open IIS and even though SharePoint is functioning properly, IIS doesn't even show the server or sites listed there. I have to do an IISRESET to rectify the situation which is less than ideal since that interrupts service on the sites.
If you have this issue, install this hotfix. It solved my problems.
This same hotfix also gets rid of recurrent event ids 6398, 6482 and 7076 related to protected memory errors.