Do you get this problem after installing the Unichrome drivers? I've been using the generic drivers because of this issue. I have the VIA CN1300 and a Liliput.
Everytime I try to install the Unichrome drivers this problem comes back up. I can get the driver to work if I set the S3 tray utility to use both LCD and CRT, but that seems to work only for a short time. I also noticed only 640x480 is avalible (you can get other options by making the control list other modes). My BIOS is set to CRT, CRT+LCD did not work for me.
I'm wondering if it is switching to TV or LCD which the monitor can't output. It's obviously changing something in the BIOS, because I have to reset when it happens.
I've contacted VIA but they are not much help here. I'm sure the VIA drivers are faster than the generic ones.
I have my setup on the bench right now, so I'm looking into this again.