Comment 8 for bug 441942

I sense confusion over how it is supposed to work, and It's unclear what "the same thing" means, so I'm marking this incomplete so we can get clearer on this.

Please add details on what kind of inbox you have (local, pop, imap, etc), what provider you use, and the sequence of events you observe.

As Ted noted above, the number you see on the indicator is not "unread" messages, but rather messages you haven't even noticed by looking at your Inbox message listing. (Can anyone point to any documentation or a blueprint to clarify the expected behavior? I've dug with no success.)

It is working that way for me, and this is what you can expect:
* send mail to self
* do not visit your inbox until you expect the next periodic check (10 minutes by default)
* watch for notifications or change in status bar indicator
* expect popup notification with # of unnoticed messages, and change in color of mail indicator in top panel
* visit your inbox in evolution, but don't read the mails
* observe that after looking at the inbox in question and clicking on an old, read email, the indicator changes color to normal, and the number of unnoticed messages is 0

For better debugging, follow the directions at "Evolution bug hunting": http://projects.gnome.org/evolution/bugs.shtml

I.e. first exit evolution and shut down all the other evolution processes:
  evolution --force-shutdown
and then enabling a debug file:
 CAMEL_DEBUG=all evolution >& /tmp/evo.log

you can see what is going on behind the scenes. You can install the "multitail" package to get timestamps on the debug lines:
 multitail -ts /tmp/evo.log