I have had the same issue over the years with TB with IMAP (Not sure about POP3) where filtering was not applied to newly received messages that were already read. The messages that are "new" but "already read" occur because I use IMAP on my cellphone as well as TB on my desktop.
Just now I used TB15 to create a filter to take messages from myself and place them in a folder.
- I wrote a message to myself.
- After hitting send I closed TB15.
- On my cell phone, I read the message.
- I then launched TB15
Sure enough the Filter did NOT apply to the new but previously read message. If I select the message in my Inbox (that wasn't filtered and moved) and do Tools/Run Filters on Message it is moved just fine.
If I do the same experiment but don't read the message on my cellphone (So it isn't marked as read) - when I launch TB15 it shows up as unread and it was properly filtered and placed in the appropriate folder.
My IMAP server is a standard Dovecot configuration running on a Debian squeeze System.
I have a suspicion it may be different behavior with POP3. I don't have POP3 set up for my account so I haven't tested it.
As for others who have posted in this thread, I believe Steve has a valid complaint that even I can reproduce (and have experienced over the years). Since new messages (that are previously read) *may* not be processed by a filter in real time, I think its reasonable for someone to suggest the Inbox be reprocessed at start up just in case. I think from the user perspective (Steve) this is a bug.
When Steve said he received email while TB was closed, I believe he meant that the email was sent, received by his server, but not processed by an email client (TB) on his desktop.