1) Most of the time that is when someone replies.
Exceptionally, when someone edits a topic or reply, even for a small typo.
The most notable instance of this side effect is when a moderator moves a misplaced thread into the correct forum... It's kind of technically correct that the thread has changed since you last read it, but maybe most of the time, you don't care about that kind of change... right? ;)

2) Yes, I found that missing too on a couple of occasions.

1) Probably not, if it's had its forum moved. I tend to view the forum through the 'Latest Posts' link, so I can't tell which forum I'm viewing anyway. What I'd noticed though, was that I could go back any number of pages of threads and they all had the coloured icon attached to them, hence my thinking that something about the upgrade had caused it - they couldn't all have seen a change.

2) With this one, I guess I'm just trying to replicate what I'm used to seeing elsewhere.It does seem slightly odd that the 'New Post' button should appear at the bottom of the page, and not prominently at the top.

Cool cool cool.
1- quick suggestion can the "new topic" button be moved to the top ? or even better both on top and bottom.
2- "Quote" is only available on the 1st post ?

Other than that, everything looks so bootstrap-ish, but thats the way web is these days anyway :P I hope it'll find its own feel along the way, looking nicer already.