In the last hour or two I've gotten green notifications for rep changes, but they look like badge notifications because there's no number:
I sometimes see this graphic appear for something less than a second and then be replaced (or overlaid?) by the number, but this stayed the same over time (a few minutes in the header, and I left the drop-down in the screen shot in place for several seconds). This has happened a few times.
(OS 10.6, Firefox 31.0 and Chrome 36.0.1985.125, no known recent changes in add-ons.)
Edit: I just got a number-bearing notification on my Android phone (Chrome), but this bug is still showing in Firefox on my Mac.