I've noticed the same issues on my Thunderbird install. With the Sept 1 release, reading an email doesn't mark it as read. If I manually mark it read, within a few seconds it goes bold again. I'll skip to the next email, and five seconds later it goes unbold. Also, deleted emails now appear in the mailbox in the web interface, but with a line through them.
Also, in Thunderbird, drafts still stack up every couple minutes if I'm working on a new email over a period of time. If I don't make any edits for a while (ie; no changes) then no additional copies in my drafts folder. If I'm editing constantly over, say, ten minutes, then I have multiple copies in my drafts folder with the various iterations. This issue has been hanging around for a few SM versions.
Additionally, the issue that made me try emClient back a few months ago: folders not seeing new emails, even if I click Get Messages, unless I go look at another folder, wait five seconds, then come back to the original folder. This works sometimes. Sometimes not. If I'm in a critical back-and-forth email period with a client I am forced to go to the webmail to ensure I receive emails when they arrive on the server.
BTW, I know some people here love emClient, but it was a total failure for me. Endless spinning wheel.
Mik MullerMontague WebWorks