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I just installed Ubuntu 13.04 in Virtualbox 4.2.16 and found much to my annoyance that the VM thought my mouse was a little higher than it actually was:

Ubuntu thinks my mouse is a little higher than it actually is

It turns out this is caused by having 3D acceleration turned on in VM Settings – Display window. After doing a bit of sleuthing I came across a forum post on with a command that did the trick nicely.

Simply open a terminal and run

VBoxManage setextradata global GUI/Customizations noStatusBar

Restart your VM and voila. Perfect mouse working with 3D acceleration!

Mouse Y-Axis working as it should

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