Thanks to y'alls help, we may be closing in on this issue. And I just found this by Joe Kissell over at TidBits:
http://tidbits.com/article/14547
Unified mailbox behavior: In 10.8 Mountain Lion and before, you could drag a message from any mailbox to the unified Inbox icon (which contains the Inboxes for all your accounts), and Mail would move it to the Inbox of the account where the message was stored unless it was stored locally and thus not in any account, in which case it would be moved to the account shown first under the unified mailbox. The same went for other unified mailboxes Drafts, Sent, Junk, Trash, and Archive. However, in 10.9.0 and 10.9.1, this convenience feature was gone; when dragging a message to any unified mailbox, you had to expand it and select a specific account underneath. Now, in 10.9.2, were back to the more convenient Mountain Lion behavior.
Gmail special mailboxes: In the first two releases of Mavericks, although you could uncheck the Store Draft Messages on the Server, Store Sent Messages on the Server, or Store Junk Messages on the Server checkboxes on the Mailbox Behaviors view of your Gmail account preferences, as soon as you reopened the preferences window, youd see that they were checked again. In other words, you were obligated to store Gmail drafts, sent, and junk mail on the server whether you want to or not. Furthermore, Mail forced you to use the default locations for Gmails Drafts, Sent, Junk, and Trash mailboxes. (That is, if you chose another mailbox and chose Mailbox > Use This Mailbox For, the submenu was dimmed.) Both of those annoyances are now gone; you can store special Gmail mailboxes on the server or not, and if you do, you can choose nonstandard mailboxes if you prefer.
Gmail mailbox order: Previously, you could not rearrange Gmail mailboxes in Mails sidebar; those at the top level of your Gmail account were always in alphabetical order (although, strangely, mailboxes nested within another mailbox could still be reordered). Now you can reorder Gmail mailboxes, but not the special-purpose mailboxes Gmail automatically creates such as Important and Chats.
Gmail AppleScript problems: If you had an AppleScript that targeted a Gmail mailbox other than Inbox or Archive/All Mail, it would fail, because AppleScript saw all the other Gmail mailboxes as being empty. Now AppleScripts can again see into Gmail mailboxes properly.
Exchange reliability: Users with Exchange accounts had found that Mail checked for new messages on launch, but not afterwards; you had to either quit and reopen Mail or take your accounts offline and then check for new messages manually (as described in this Apple support article). That has now been fixed.
Addressing to Smart Groups: The Contacts app lets you create groups of addresses for example, a Family group that contains the contact records of your family members. You can type a portion of a groups name and Mail autocompletes it just as it would for an individual name. Autocomplete does not work for Smart Groups (so, that much hasnt changed since 10.9.1), but now, if you type the entire, exact name of the Smart Group and type a comma or press Tab or Return, Mail at least displays the group name in a nice blue bubble, and the Smart Group does in fact work Mail sends the message to the correct addresses.
