According to those settings TB should leave a copy of everything on the server (for the selected account) I couldn't help noticing that you're using Yahoo mail, is that a webmail account that's being accessed via a web/pop proxy or is it a genuine pop3 account? In the first case I'd guess that it's the interaction between your proxy and Yahoo, in the latter case I can't give a proper reason, maybe if you're using some other proxy (anti-virus, anti-spam), but I don't know.
Besides, you're saying you configured TB to leave a copy of all messages on the server and that it isn't doing that. Does that mean that TB leaves a selection of the messages on server or none? The first case could be caused by selective download filters.
__________________________________ I'm just a user of The Bat! I don't work for Ritlabs.
I don't know what's causing the problem then. For myself it has been a while since I kept all mail on the server indefinitely, but I'm still using the keep mail on server for one day option and that's working flawlessly. You could try whether that works for you. What version of TB are you using?
__________________________________ I'm just a user of The Bat! I don't work for Ritlabs.