OK... Why is it you always discover the problem 30 minutes after you give up and create a post?!
Problem resolved. Dual versions of VBP on the system. When bringing up the project in the GUI, it launches using the latest version which is 6.2. The scheduled task was not updated to use the VisBuildPro6 path and so was using the older version. Step differences where erroring out with the older version because of some small changes that are not available.
Hope this helps someone.
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