I ran into this issue as well, basically anything in the top inventory row has this tool tip flicker. Turning Vsync off just slows the rate of flicker for me. When the flicker is slowed, it looks like it's caused by the UI having trouble deciding what height to make the tool tip popup window ( the bottom is fixed and the top flickers up and down causing the text in the window to flicker also due to vertical auto-spacing. The closer to the top of the tool tip window the text is, the more flickering occurs because of the greater shifting due to the text auto-alignment in the window.
Switching the resolution to a mode with 60Hz refresh rate appears to eliminate the flicker, but I don't want to do this since the only option to run at my monitor's native resolution of 1920x1200 is @ 59 Hz.
I was able to get the specific incident of flickering to go away by applying a resolution that wasn't 1920x1200 @ 59Hz, then exiting the game, relaunching the game, then switching back to 1920x1200 @ 59Hz. I haven't figured out if adding the -popupwindow argument to the launcher has any effect on the bug. We shall see if it shows up again.