The additional libraries path in Tools -> Configure Paths does not seem to be being scanned for libraries on startup nor when the additional library path is changed. The jar and xml files I am trying to reference in the additional path are fine as they show up in the Libraries tab if I copy them to the Libraries folder.
Yes, I'm sure. To make quite sure I moved SQL.jar and SQL.xml out of Libraries, where they got recognised, to C:\Temp and set the additional libraries path to point to it and they don't get picked up on restart.