Same problem here. I have been using Gmail IMAP for at least a year and this just started recently. Very annoying. Furthermore, some outgoing messages get stuck in the Outbox and end up becoming duplicate sent messages. Sometimes the same message will send three or four times! Also annoying for the people I am corresponding with.
For interest.. here are Google's recommended settings for Apple Mail. Going to try them to see if it helps.
+From the Mail menu, click Preferences > Accounts > Mailbox Behaviors+
Drafts: +Store draft messages on the server > do NOT check+
Sent: +Store sent messages on the server > do NOT check+
Junk: +Store junk messages on the server > checked+ +Delete junk messages when > Never+
Trash: +Move deleted messages to the Trash mailbox > do NOT check+ +Store deleted messages on the server > do NOT check+
Not sure that this helps though, especially because I like to have access to drafts on multiple devices. The whole point of IMAP!
Apple Mail has always been a bit of a dud. Lately it seems the quality control at Apple is not as good as it once was. Sad.