Has something been changed with the scout reports?
Yes, the RegionDetails script (which also generates scout reports) was converted to Doctrine. This should not have changed any functionality save for adding the post-rebalance food/gold numbers.
The sections aren't divided into tabs anymore.
I do not experience this behaviour. What browser are you using?
Possibly related somehow - I can't mark messages anymore, or unmarked already marked ones.
That is only related in that they both require Javascript.
Have you, perchance, disabled Javascript in your browser?