SublimeText2 (Build 2.0.1 / 2217): Occasionally, all of the flagged words (potentially misspelled) in spell-as-you-go blink and disappear when using a dark background. The words reappear when moving the cursor to a different position, or by just waiting a second after switching keyboard focus back to the ST2 application.

Using a white background can prevent the words from disappearing, but they turn bright green temporarily.

There is now a viable workaround – a spell check alternative.

github.com/phyllisstein/CheckBounce