This sounds quite similiar to what happens on my ThinkPad R61 with Intel GMA 
X3100. I use KDE 4.3.2 under Debian Testing AMD64.
When I boot with an external TFT at VGA and switch from 1024x768 to 1280x1024 
(native resolution of the external display) the cursor becomes invisible on the 
external screen. When I switch back it reappears.
After some time it becomes visible again when I leave the resolution at 
1280x1024. I'm not sure why exactly ... when I looked on the TFT it was 
suddenly there. In all these instances I was working in a terminal window 
(yakuake), but I have to verify if that's the reason.
I had no problems with Kubuntu 9.04 and the external display.

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[i945GME,nomodeset] mouse cursor invisible
https://bugs.launchpad.net/bugs/475917
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