I noticed a strange pop-up menu appearing when I left my Intuos 3 pen resting on the tablet. The same thing was causing unacceptable lag (a good half a second) when drawing in any application.
Apparently it's something that Windows has introduced to help tablet PC users access a right-click menu when using a touchscreen.
I did some digging and found that it can be switched off, using diverse and nefarious methods depending on which Windows OS you're on:
http://forum.wacom.eu/viewtopic.php?f=9&t=1091
Thought it might help anyone else with the same issue.
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If you look for Tablet annoyances begone you should be able to find it.