I know that in the Behavior options for the project, I can configure SCO to exclude schema names in the deployment script. However, this can be confusing if the target schema differs from the connected user on the project.
For example, if I configure the project to connect as SYSTEM and have it compare a source schema (DS2) to a target schema (DS2DEV) and I exclude the schema name from the deployment script, the deployment wizard runs as SYSTEM and installs the objects in SYSTEM instead of DS2DEV.
I understand why it does this (after all, I told it to exclude the schema name), but there's no indication on the deployment window as to which user will be running the deployment script.
I know that I'm supposed to remember how I configured the project -- but I think you need to highlight the "Run As" user in the deployment window.