This sounds like Outbound Rules.
In the Outbound Rules have you specified "Calls from Extensions" or "Select Extension Groups"?
If yes remember that when the Conference Server is making an external call, it is neither calling from an Extension nor from a Extension Group, so it will never match any Outbound Rule that has any of the above 2 options set.
You would also check the activity log to see if an Outbound Rule is being matched or not.