I saw this with Waves plugins specifically some time ago but nothing lately. Of course, the original post stated OS X 10.5.5 which is not even close to supported by WaveLab 9.
Sorry, I see that you’re using El Capitan. Do you see the disappearing cursor issue with all plugins randomly or just a certain plugin or plugin vendor?
Are you using WaveLab in 32-bit or 64-bit? Any difference with VST2 or VST3 versions?