I now see that this is a very old post! Did you ever get a solution to this?
I'm having the same problem lately. I've tried recreating the DataSource connections but that doesn't seem to help. All login information has been checked twice and I can make changes with other DB workbenches.
To add to this note, I am now sure this is a ColdFusion 10 related problem as I can't even make changes to the very simple Apache Derby database that is used in Ben Forta's CFWACK book series... I also get the coldfusion.sql.DataSourcePermission error.
I'm running CFBuilder 2.0.1/CF Server 10 on Windows 8 64bit Pro.
Did you check sandbox security in CF Admin? Sometimes that can throw a spanner in the works.
I wasn't using sandbox security but that was a good suggestion as I hadn't checked that!
In the end, I reinstalled CF Server again by downloading CF10 from Adobe's site along with the Mandatory update (you'd figure that would be on the public download now but it isn't!).
I then updated to "update level" 13 (yep, got that terminology from the settings summary page) and we're back in business.
I'm guessing this may have been a problem with one of the security updates.