Mail not moving messages or deleting from server until application quitted

I have an Outlook.com email account. When I delete messages or move them in Apple Mail, the change is not reflected on the server until I quit the program completely. This isn't happening with other actions. Mail is immediately marked as read or flagged on the server for example. When I move or delete messages in Mail they actually show up in both the original location and the new location until the application is quitted.
Anything I can do to fix this?
OSX Mavericks 10.9.1
Apple Mail 7.1

Hi Thomas
Yes...personal folders are mailboxes I've created to organize my mail. I know as a fact that this messages still are on the server even after moving them to "personal folders". anyway I think i can get around this issue by rightcliking on the account and then getting account information. I can then filter by "removed from my mac". at that stage there's an option to select those messages and "delete from server"...I think this will work...will try now.
Thanks for your help

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