All seems to be working fine for me (unless I'm missing something). Firefox, preference=flat mode.

Folders with no new posts (since my last view of the thread) are white.

Those with new posts: the folder is yellow, all horizontal cells are a distinctive gray (more so than the alternating white/gray), and the Replies column shows the number of new replies (since I last read the thread) in parenthesis.

Once I return to the view showing all Subjects, and hit Refresh, the folder turns white, the gray goes away, and the number in parenthesis disappears, and the total number of Replies increases accordingly.