I am also having similar issues. I have a model tool (combination of different tools and scripts that I combined in a single ModelBuilder tool) that runs great when ran manually, but every time I run in as a scheduled task or in the "History" panel, I get a bunch of Errors: 000725, 000258 & 000670 (which should not be the case as I have a precondition to delete all feature classes in my workspace before running the parts where I produce the new updated data).
I tried separating deleting the feature classes as a separate tool that runs before running the data update tool but it did not help also. Pretty frustrating to troubleshoot.