One of the problems with running the Skype-to-Asterisk bridge (chan_skype) in a VM is that the bridge stops working after a period of inactivity. It's been driving me bonkers for a week now as I've researched Skype, chan_skype, and Asterisk heavily, looking for the timeout. Then, on the way home, it hits me: the instance of Skype is actually running on top of VNC.
The short version: tenative (I haven't proven it yet) kudos to Bruce Nepple for this post which discusses setting VNC's timeout option. Hopefully this will fix it.