I hate to criticise since you've created this great program, but why not just simply make the install an MSI?
Either way, my solution was to export the settings I wanted into a regfile, then merge that before the install like so:
regedit -s ImgBurnSettings.reg
imgburnsetup.exe /S
Save the text file as "SilentInstall.bat" and you have a batch file which automatically imports the regfile and then kicks off the silent install. This works well with deployments via SMS etc. I realise you say don't export all the settings because you change them but since I've tested version 2.4.4.0 that version is all I will deploy, until 6 months later or so where I will just export the new settings set by the new install again.
Also, is there any way to use ImgBurn as a non-Administrative user?