At least on my Tablet PC, when I write short, fast strokes, Windows will interpret it as clicking on the Flash applet as well and will subsequently show a round circle to indicate where I supposedly 'clicked'.
It might also happen with external tablets. I sold my Wacom Bamboo when I bought my Tablet PC, so I can't check.
Here's what I mean: http://i.imgur.com/ZP4eW.png - it'll start small, and grow while fading out.
Anyway, in Vista, you could turn it off in the Control Panel. In Windows 7, Microsoft moved the setting deep inside the Group Policy Editor. If you're like me and don't like the circles, here's how to hide them. The benefit of this is that you can still use the pen as a mouse.
1) Open the Start Menu, type "gpedit.msc" and hit [Enter]
2) Go to User Configuration -> Administrative Templates -> Windows Components -> Tablet PC -> Cursors
3) Double-click "Turn off pen feedback"
4) Set it to "Enabled" and click "OK".
The change is applied instantly. You can also return any time and undo it by setting it back to "Not Configured".
Note that this also turns off circles for touch input if you're lucky enough to have one of those fancy tablet/touch-combo Tablet PCs.