Setup.exe copies 'Setup1 files' instead of 'Bootstrap files'

An installation package I have created using the Package & Deployment Wiz fails to install. Setup.exe first copies across all the files in the Setup1 files section of Setup1.lst (instead of the Bootstrap files section) then insists on a reboot. After reboot it does more or less the same ting again but copies less of the Setup1 files across after this.
Setup1.exe never starts.

I dunno.