I spotted that when I clicked reply to a thread, and it prompted me to sign in, when I was returned to the awaiting reply box the presence indicator was not changed to green.
Short response: I've logged this to be improved:
Longer response: I'm told this is likely a cache/timing issue caused by your online presence updating effectively after the form is rendered but the message of your presence change occurring before your browser's socket/live connection is attached (so you miss that update). A refresh should show the correct status, but the initial reply form rendering is going to be timed such that it is incorrect in some situations. While expected to be a rare condition, I was also able to reproduce it pretty easily, so I logged the bug above, if only to shortcut the "am I here?" question.