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For each new instance of VBP (the GUI app, console app, or creating via the object model), it will normally start at the first project step when performing a build. Some things that could affect this:
1) If 'Tools | Application Options | General | Persist build status when saving project files' is checked, the completion status of the steps will be saved with the project. If that build is opened and started again, it will start from the beginning, but will skip the steps marked completed.
2) If a build is initiated via script code, the startType and startIndex parameters of the Start method will determine which step it starts at.
Assuming #1 is unchecked and you are launching either the GUI or Console app from a Scheduled Task, I don't see any way that the build would not start from the first project step. If you could provide a sample project + scheduled task info to reproduce this behavior we can certainly investigate. Also include the info from Help | About | Install Info in VBP, and the files listed in Tools | File Locations that exist on your box.
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