OK, quick update on this issue (was chatting with a couple of the devs on #maemo). How it should happen (apparently, I could have misunderstood), is that the read status is updated either when switching folders or closing Modest. They delay the update until either of those instances (presumably) to reduce cpu load/ram usage/network usage/ whatever.

[7:07am] <sergio> if you mark a header as read
[7:07am] <sergio> it won't be updated in the server
[7:08am] <sergio> until you select another folder
[7:08am] <sergio> or close the program of course
[7:08am] <sergio> because we delay that update until that

What seems to be happening (for some people, anyway) is that it only updates when you close Modest (in my case and in X-Fade's case specifically) and not when you change folders.

Evidently it was something that was "fixed" previously and may have cropped up again or wasn't fixed in all cases. If people experiencing this want do a little more testing (when/if updates occur, whether manually marking as read behaves differently than actual reading, etc) and report any finding to the bug #2987, it'll help the devs pinpoint the issue and get us a fix.

In any case, the issue is being looked into.

For anybody that's interested in seeing the full conversation, it's from 14:00 onward here.