Mac Mail Problems

Have you repaired the disk permissions since doing any updates to the OS, or has mail always behaved like this for you?
 
I always had to force quit Mail on my iMac and MBP (both 2011). Happened with Lion and Mountain Lion. That said I'm now using a new retina MBP and it is fine
 
No problems here.

It sounds strange (and frustrating) that this is happening.
 
Several macs here as well, with at least five accounts on each mac. No such issues. However it reads like it is still trying to do something when you shut it down or exit. Have you ever looked in the log files to see what it is doing?
 
What version of OS are you on?
Are your emails POP3, IMAP, or MS Exchange?

Create a new User account with Admin Privs, log in, and set up one of the email accounts in it.
If it works, your Mail app is fine, and it's likely to be a corrupt .plist in your Preferences folder.
If it's the same, then you might have an app or system file issue, if not a disk one.
Use Verify on the drive in Disk Utility - if you get green text at the end, it's fine.

Short of something more wrong, a free utility like Onyx or Ice Clean would be useful to install and run, clearing the cache and logs.
Beyond that, then you're into Disk Warrior or TechTools Pro 6.
 
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