I am also experiencing this problem using VirtualBox 4.1 on Ubuntu server 11.04.
The issue was previously reported
to the author of phpVirtualBox, and I created a ticket of my own
over there as well. He reckons it is not a problem with phpVirtualBox and has been unable to reproduce the problem himself. He suggested a change to the vboxwebsrv timeout, but it did not make any difference for me.
All reported occurences that I can find were on Ubuntu hosts, so I'm wondering if it could be something in Ubuntu that is causing it?