I'm really not sure which bug I'm talking about (i.e Bug 502370 or Bug 518581), but I have noticed a few things here:

0. (Yes, zero) It seems to me that TB doesn't expect mails to be marked as unread on the server when it hasn't done marked it itself. Put simply, TB is coded to believe that only it is capable of marking a mail read or unread while it is running. This is expected behavior and this is not where we want to fix this bug. (Unless you want TB to check the message ID, which may or may not be a nice thing to do. But read on, I think this issue can be fixed in a different way)


1. This can happen backwards as well. I can read the mail in All Mail and then check the mail in the other 'Labels' that mails is in and the mail will not be marked as read in these other Folders/Labels. If the initial problem is understood, this should be as well, because one of the reasons (I'm coming to the other) this problem exists is that TB doesn't recognize the Label system, and tries to apply the folder system to GMail. By this logic, the reverse issue should affect us in theory, and it does.


2. This bug is not 100% reproducible. If I read (say) 10 unread mails in my Inbox, reading the first 7 for a long time and quickly glancing over the last three, just to make them read, and immediately go to All Mail, TB checks for new mails and marks ONLY the last three as read, leaving the first seven that I took a long time to read as unread. When I have a mail in three Labels, and I read it in one, it is often marked as read in one of the other two folders while unread in the last one.

Here's my guess, for why TB behaves that way:
It does seem that when a 'folder' is not opened for a long time, the type of checking that TB does (in the background) is different from the type of checking that TB does when I open a folder (in the foreground). If a "background"/automatic check is done on the server, TB seems to check for new messages only. It doesn't check for any other changes. When it does a full check, only the changes since the last "check" seem to be recognized.

How this can be verified (over the next couple of days, I shall try these tests and post the results here):

  a. Disable all automatic and periodic checks ("Check this folder for new messages" in the folder preferences) on one folder. Read a lot of mails that are in that folder from "All Mail" and wait at least ten to fifteen minutes. Now open that folder. If this theory is correct, TB will correctly mark all read messages in that folder as read.

  b. Enable automatic checking of a folder and change settings to check every minute. If this theory is correct, this bug will be far more reproducible and should happen for almost every message. At the moment, this is reproducible but doesn't happen for all mails.

To summarize point No. 2, TB, I think, checks the server only for new mails when it does an automatic check, but when it does a proper check (when you open that folder) it looks only for changes after the last automatic check.


3. The list of read/unread messages syncs itself properly if I restart TB. Since this is the first time I'm checking in that session, I presume TB does a more thorough check and brings everything up-to-date. There is no issue of having unread messages that I've already read in the long term. Sooner or later, everything sorts itself out. It's only *during* a session that the problem holds.

Hope this problem gets fixed (and that this isn't marked "invalid" ;) ). I will be willing to try things out if any help is needed to find what is causing this.

I am running Ubuntu, using TB 3.0.2 from Mozilla binaries packaged into a PPA (ubuntuzilla): 

Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.9.1.8) Gecko/20100216 Thunderbird/3.0.2

I have seen this bug on Windows also. 

Please mark as CONFIRMED, Platform: All. I began using IMAP only after TB3 came, so I cannot confirm the versions that are affected.