Well, since this was my thread to begin with, I might as well answer.
Enable this option: Tools>Application Options>Logging>Delete log file at the start of each build.
Note that for some reason, if you restart the build in the GUI over and over again, even if you reset the status of all the steps, it will still retain the previous log (and builds). You will have to close VisBuild, reopen it, and then start the build again to overwrite the previous log file.
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