When the FB3-SE is ordered, and no "specific communication" takes place (i.e. a dialog between the customer and Pangolin, determining how and where the FB3-SE would be used), the assumption is that the FB3 will be used inside a projector, in a dedicated configuration, with the scanners knowing full well and good how they will be used and the voltage level to expect.
If, on the other hand, some dialog takes place, and an understanding is developed that you need differential output from the FB3, or that the FB3 might be used outside of a projector, Pangolin would include (or sell you) a special daughterboard to develop balanced output signals. The daughterboard is very small (smaller than a postage stamp) and so it might go unnoticed.
We suspect that you have one FB3 without the daughterboard, and one with. If this is the case, you could purchase a daughterboard from Pangolin. The cost is minimal.
Best regards,
William Benner