OS X Mavericks changed the way it handles Google Mail accounts. Power users who have hidden the All Mail folder from appearing in Mail (via Google Mail’s Settings > Label) are experiencing the strange bug where messages are reappearing in the original mailbox after filing.
The solution is to show the All Mail folder in IMAP
Checking this box will cause OS X Mail to download all your Mail again, a process which can take a long time if you have a lot of email. It’s the only known workaround at this point to make filing work properly, whether you are using MsgFiler to file messages or drag and drop in Mail.
MsgFiler 
No, this is not the workaround for me. I always had ‘all mail’ visible, but now I switched to Mavericks on my MBAir I still have the strange bugs that means when I move or delete a mail on the Mavericks machine it reappears in the inbox, and if I move or read or delete it on a Mountain Lion machine the changes have no effect on the Mavericks machine.
What happens if you move the message manually in Mavericks Mail, either through drag and drop or the Move To menu command? Do the messages occasionally reappear in the inbox?
Doesn’t fix – already showing.
If you file messages using drag and drop in Mail or using the Move To mailbox menu command, do the messages reappear in the original mailbox?
Can you make sure that Mail has completed syncing all of your mailboxes? Look in the Activity dialog.
I have been getting a strange glitch where it moves the message and then the same message re-appears for about 2 seconds and disappears again. Probably not the worst glitch but I am spoilt. I have been using this app for ages now and I file my messages at an incredible pace since I batch file at night. This glitch is slowing me down.
if anybody can help get it back to the way it used to be that would be fantastic.
S Popat:
I think it’s another Mavericks Mail behavior difference over Mountain Lion Mail. If you open up Mail’s Activity Window, you can see what Mail is doing at any given time with respect to communicating with your mail servers. I just went through and filed 6000 messages over the weekend and experienced the same thing. Eventually the messages were filed, but they occasionally popped back up before disappearing from the original mailbox.
This also happens for me if I drag and drop between the message list and the mailbox list in Mail. So, I don’t think it’s isolated to the way MsgFiler communicates with Mail.
Hopefully this and other problems with Mavericks Mail will be addressed in a future update. I encourage you to write a bug report to Apple either here:
https://developer.apple.com/bug-reporting/ (requires developer account)
or here:
http://www.apple.com/feedback/macosx.html
I do get the “disappear-reappear-disappear-then filed” that was mentioned when filing from my inbox. I also found a new problem: if I filter my emails first with smart mailbox and then go to file the message, the message disappears and then reappears, never having been filed.
Mark – Are you saying it re-appears in the Smart Mailbox or in the original mailbox?
I have a smart mailbox that filters my inbox (e.g., employee emails). When I file a message from the smart mailbox, the message reappears in my smart mailbox as well as my inbox.
Mark – and this worked previously in Mountain Lion? What happens if you file the message using drag and drop in Mail or the Move to mailbox menu command? Does the same thing happen?
Yes, all was fine in Mountain Lion.
I just tried the drag and drop from my Smart Mailbox and the same problem happened (came back in the Smart Mailbox and the inbox as well). So, it appears to be a Mavericks problem.
I am getting this same behavior of re-appearing messages after filing with an Exchange account too, so it does not seem to be just limited to Gmail. I have less ability to change backend settings so if you all know of any way to get things working in Exchange too, I am open to trying anything. Hopefully Apple will send out a fix soon to address these issues. Thanks!
Hi Adam-
Any thoughts on the new Mail update for Mavericks as it relates to Gmail and Msgfiler? I have been holding off on the update. Thanks.
If you were having problems with Mavericks Mail and Gmail, it’s worth trying. I still see the occasional disappear/reappear/disappear filing behavior, but messages do get filed.
Hi Adam… I’ve been having the disappear/reappear/disappear behavior for some time. The trouble is that when the message reappears, mail “selects” (highlights) it which then has the effect of deselecting the (next) message you’re actually trying to move. My current work-around is to take all mailboxes offline, file the messages, then take everything back online. Which often works, but sometimes doesn’t. Any better suggestions than this?
Dan – I’m not having the problem where the next message is ultimately deselected. What are the specs on your computer? You’re using the original plugin or MsgFiler 3 and the Engine?
Do you have MsgFiler set to stay open after filing or is it hiding after filing? Can you try the other method and see what happens?