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.