The settings I was talking about were the different PAL and NTSC options on the Roxio capture software.
As well as the widescreen, 16:9 and 4:3 ratios on the Wii. Also the 50Hz, 60Hz and EDTV 480p options on the Wii.
Whenever I changed any of the above, the screen portion cut off would also change randomly.
Something I forgot to mention was that, if I change the sound input from the Roxio unit to the microphone in my laptop the screen is fine, but unfortunately then I have none of the audio from the game so that's not quite a solution.