I believe I've finally found an answer to the HDCD question. According to Stereophile Jay's may be using dither with 16/44. The HDCD signal is passed only if the information on the HDCD encoded CD is passed in its original form. So, if dither is applied, or if the 16/44 signal is upscaled, the HDCD encode won't pass.
Sometime back I replaced my GeerFab with an Audiopraise Vanity Pro. The APVP was a game changer. The HDMI signal sent from my Oppo to the APVP, then to my Berkeley DAC via AES/EBU, resulted in better CD sound quality than from the Jay's directly to the Berkeley. It makes no sense, but it did. I sold the Jay's.