Filters are auto run on new unread mail that is downloaded to the Inbox for that account. As IMAP mail accounts see a remote view of the server, the folders are in effect one and the same regardless of how you view them. As you had previously accessed the server and read the email, it will no longer be new unread mail as that setting will have been set on the server. As a test, I suggest you mark the previously read emails as 'unread' at the time of reading whether this is via a phone or webmail and see if this triggers the filter when you view emails via Thunderbird.