MacFan7, I have been experiencing your exact problem since upgrading to Mountain Lion.
I have ALWAYS had the Mail client set to manual and have about half a dozen POP accounts. When I return to my computer after some time and it has, as such, slept, I wake it up to find that the Mail application has seemingly tried to acces email accounts but something else has (properly) timed out and prevented it from accessing the Keychain to get the passwords. This seems to wedge the Mail application.
I assume this is a bug and, to compensate, will quit Mail before I leave the computer.
The Mail in Mountain Lion is either more buggy than it should be or has a number of subtle and very annoying UE changes - I think it's both! Something as fundamental and important as email should not be left to junior or inexperienced engineers; if this is not the case, significant reviews should take place before changing such an important facility....
Should this (and other problems) not get fixed, I will have to evaluate alternative Mail clients.....
aps.