Help with the epiphan vga2usb frame grabber
I'd first try some different software to see if it is a hardware shortcoming or not.  If it is a hardware short coming, I'd go for a different approach to getting the highest quality signal possible.

Based on your needs to operate with minimal gear, taking the fewest devices and trying to keep the best quality, I'd probably try and go with something like an HDMI capture device like the Black Magic Intensity (which will work over either Thunderbolt or USB3) and then for dealing with analog signals coming in, I'd probably pick up a scan converter to handle the analog signals.  

DVI's pretty much cross compatible with HDMI, so if you can get either DVI or HDMI, you should be able to use it with the Intensity directly.