Ok. This is happening because some of the project names do not match their filename, which is not currently supported correctly in the Make VC6 action. For instance, several projects have a dependency on API, but there is no API.dsp in the workspace (it probably has a different filename). Apparently this doesn't happen very often since it wasn't discovered until now!
We will correct this in the next release, which is currently in beta, and send you a link to the beta when this bug has been fixed.
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