Since switching from Wise to AdminStudio I have not been able to workout how you perform a capture of an applications first use settings to save in a transform when the package is originally an msi?
Any ideas which tool I should be using, its probably staring me in the face or does this feature not exist in AS?
You can use repackager. You then choose installation monitoring (it gives cleaner results for what you want) and the application's executable you want to get the settings.
Don't run the application manually. The repacker will run it for you. Then the user do all the actions he want to reproduce to everyone. Just that. Careful with passwords or any personal settings.
I recommend that you analyse carefully the results and clean any personal information or change it.