Hi Dave,
Maybe you have done these things, but here are two ideas:
1. Before beginning the acquisition with PfE, acquire an EDS spectrum from Pathfinder with the desired low energy cutoff. Then use PfE to acquire.
2. Create a Pathfinder project that has acquired spectra with the desired low energy cutoff. Then create a new project in that project and acquire data with PfE.
Let me know if either of these options help.
-Steve