Also reproduced in snapshot 13w11a vanilla single player.
In the item bar, I've only experienced flickering in the first stack, regardless of its item slot, so if, for example, I've got three wool in slot 6, and two seeds in slot 7, the 3 on wool will flicker, but not the 2 on seeds. But if I rearrange the two and put seeds first, then the 2 on seeds will flicker, and the 3 on wool will stop.
Happens regardless of video settings or game mode.
Have not experienced flickering in any other gui component.
I'm running MC through 64-bit java on Win7, also using an ATI video card.
i went back to a previous version of java! so java 17 was the issue, it seems.