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Regarding the skipped steps, are any of the parent steps unchecked? If so, and "Tools | Application Options | General | Implement nesting of 'Include in Build' step flag" is checked (the default), any child steps of an unchecked parent step will be skipped. Either ensure all parent steps are checked or change this option. If not, send/post a project the reproduces the issue you are seeing.
On the 'object reference' error, I assume you're building a Make VS.NET action? That error usually means that the action encountered something unexpected while parsing one of the project files. Send/post the .SLN + consitituent project files in question, along with the .BLD file that builds them and we can take a look.
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