There are 2 issues here: 1. When you open an account in thunderbird it opens new inbox drafts deleted etc folders for each account, and message filters only work for the accounts they are set up in. Even if you select <view/unified> there is still a maze of different user account folders in your navigation pane. If you don't want this, the only way I could work around was to create the user accounts in windows live or outlook and import them <tools/import/settings/> - laborious! *You need to delete any accounts you manually created in thunderbird <tools/user accounts> before you import or the ones you already created will not be replaced and will still be separate. Result: you get ONE of every folder, which receives email for all accounts, and ONE message filter setup! And user accounts still show up un user accounts, but not the folder navigation pane.

2. If you don't want to do the above you can try <view/unified>. There is also a favourites option. If so, you need to set up your message filters for LOCAL FOLDERS unless you only want them to work on one account.