Option notifying of new messages does not seem to work with IE.
Also I sometimes get weird little windows popping and dissapearing before they're loaded enough to read them. They do seem like the "welcome" site window, though. These appear on both IE and Chrome.

PS Buttons under posts are still misplaced for IE.

Which version of IE?
Do you mean that threads you subscribe to don't show up in your subscribed threads list? Or that there is no email notification? If the latter, yes, that's been turned off for years.

No, no, I mean private messages. There's an option "show new private message notification pop-up". It worked before.

IE version is 9.0.8112

This should be fixed now.