Some video capture drivers dont save your setup. For instance, some video capture drivers always start up expecting the video in signal composite. If you are using S-Video as your input signal, you will need to go to Edit/Setup/Video/Source and set your input signal each time you start VIS.
This problem of retaining settings is part of the video capture card software and cannot be controlled by VIS.
You may or may not have problems with initial settings on your video card. The only way to know is to just set up your card and then exit VIS, start VIS again and check out the settings to see if they are still like you set them.