I've search long and hard for a solution to this problem...but I've had no luck.
The problem is that occasionally some clients will begin to get the security pop-up for autodiscover.domain.com. This happens after Outlook tries to contact all of the possible Autodiscover sources and is not able to connect to any. We do not have a sans certificate, so this is why the security error pops up.
If the client computer is restarted, everything begins to work fine again, and Outlook is able to autoconfigure itself.
All help will be greatly appreciated!