I feel this is a usability flaw in Gmail’s "Mark as read" contextual menu item.

For all the contextual actions, once the action is done, the checkbox status is turned back to default - i.e. not-checked.

However when you "Mark as read", the mails remain marked i.e. checked, even after the action has taken place. This means the user has to manually un-check all the mails before he takes another action. Thus he is always at a risk of taking wrong action on the un-intentionally checked mails.

I think, once the "Mark as read" or "Mark as unread" is done, the checkbox status of the mails should be turned back to the default. This will provide users a predictable and expected system which is consistent with other options of simmilar nature.

Abhishek