The "mark all read" function literally marks all threads as read, whether you have actually read them or not. You can still access any of the threads you missed by using the "archive" link, but clicking "mark all read" will clear & archive that particular forum's posts for you. All new posts will show up and remain until "mark all read" is selected again. At least that's the way it's worked for me in the past. The last part of your question will need to be addressed by the programmers, because I don't know, sorry!
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