I have configured a number of folders in Hotmail where certain e-mails (like newsletters) are forwarded to. I installed Thunderbird on my home laptop and those folders are never synced, just the way I like it.
On my work laptop however, I have the same configuration but more folders are synced and I get a notification every damn time when I get a new e-mail. This annoys me a lot (because I have +30 unread mails so the overview of new mails is lost) and I don't seem to be able to find out how to ignore certain folders. Plus, it's weird that it works on the one system and not on the other.
When getting new messages for this account, always check this folder is unselected in the folder properties. The Thunderbird version is Thunderbird 24.3.0 and I use Ubuntu 12.04.