Thanks Aaron,
Regarding item 3. The error message is actually supposed to be more of a warning message.
When you add an object from another database (in this case, the comparison database) it also scripts the permissions and tries to apply them. I suspect that in this case, the database you were adding the object to perhaps did not have the user to which to apply the permissions.
We're actually going to be changing this implementation so that when you're adding objects to a project you get the same status window that appears when performing deployments. In this way, any errors or warnings appear against each object.
I'll make sure we address the other points you've raised.
Thanks,
SQLDBcontrol Support
support@sqldbcontrol.com