I have a model that truncates a table and then copy's rows over to a GDB and applies privledges. If I am in the edit of model builder and run the model it deletes all rows and copy's the new rows over. If I run the model by just double clicking on it in Catalog it runs and then my tables disappear.
I'm glad it works when I run it manually but I'm not sure why it wouldn't run the same in an automatica environment.