Kurt,
I have the Pio 1110HD, which has virtually the same media receiver.
A few points.
First, the user manual that comes with the panel doesn't show the HDMI inputs on the back of the media receiver. They were added after the user manuals were finished. I received a one-page addendum in my media receiver box that shows the HDMI inputs.
Second, you are correct; they are inputs (assigned to Input 1 and Input 3), not outputs. I have speculated that the HDMI format could support daisy-chaining similar to iLink (i.e., all ports are both inputs and outputs), but I haven't seen anything official on this issue.
Third, the white system cable is a DVD-D (dual) format cable in shape, but it is strongly suspected it is not a DVI-D compliant output. It is most certainly NOT an HDMI output. Instead, it carries a proprietary Pioneer format that is solely used for connecting the media receiver to the panel. There have been other threads speculating on the format, since the DVI spec permits 8 bit colour, but the latest Pio's have 10 bit colour. The other end of the white system cable is also a DVI-D format input, but I doubt you can stick, say, an STB DVI output straight into the panel bypassing the media receiver (nor would I recommend it). The black system cable appears to be a sort of parallel communication interface (it looks like a small-form centronics cable). I suspect audio information is sent to the panel through the white DVI-D cable, but it could also be sent through the black cable. I don't use my 1110HD for audio (monitor only), so its a moot issue to me. Bottom line is both system connections are only for connecting the media receiver to the panel.
Fourth, there was a recall in early 2004 on Pioneer displays in Japan only. The issue was related to solder strength in the circuit boards, not the HDMI format (see
http://www.pioneer.co.jp/press/release131.html ).
Fifth, the current Pio displays use first generation HDMI. I understand there is a second generation out now, but an increment in the generation of HDMI would not lead to a recall (wouldn't that be nice!). Perhaps this is what the sales guy had heard.
Sixth, I looked at the picture of your media receiver. Although it is difficult to make out, it appears that you have the input coax cable going into Antenna B input and the small gray coax shunt connected to the output of Antenna A is connected to ???. Depending on what you're trying to do, the recommended set-up is to put the coax input into Antenna A input, then hook up the small coax shunt between the output of A and the input of B. The output of B remains unconnected (as shown in your picture).
I hope this helps!