Verify that your car's antenna booster is getting at least 12V. Subaru's booster amps don't work very well with lower voltage (and many aftermarket HUs only provide 11V, and/or the voltage can drop if you're using the HU's same output to trigger speaker amps).
Some "micro bypass" (parking brake bypass) devices warn you to not connect the HU's amp trigger output to both the bypass device and the car's power antenna lead (antenna booster). Apparently, some bypass devices don't play well with the booster amp.
In any of those cases, power the booster amp from the +12V Accessory lead on the car's radio harness (usually red wire on aftermarket harnesses).
I suspect Subaru added the diversity feature to many of their HUs due to the antennas being lower and smaller (where long ago they were taller rod antennas -- either manual or motorized).
Tying the two antennas together won't work. That will wreck the impedance, making things worse.
The twin pins on the round Nissan-style plug are indeed the center conductors of two separate coax cables, one for each of two antennas. The ground contact is on the outer body of that round plug.
You might want to verify that you have good continuity (as well as no short to ground) on the center lead of the coax antenna cable, all the way from the output of the booster amp to the tip of the Motorola plug on your adapter.
If you follow the OEM antenna cords down to the floor below your HU, you will likely find a normal Subaru-style AM/FM antenna plug (gray, rectangular plastic), like shown in
this thread (the HU shown there is from a 2010 Legacy, but later USDM models still have the gray plug at the floor, and a "feeder cord" bridging from there to an antenna socket on the rear of the HU). If your car has that gray plug, you could use a single 18" Subaru antenna adapter instead of the two pieces you have now (gray Subaru to round 2-pin Nissan + round 2-pin to Motorola). Reducing the total length and number of interconnects can help improve the signal strength a little.
Another common problem on wagons is that the coax antenna cable inside the flexible conduit at the hinge eventually breaks. Search and you'll find more than a few threads where people talk about repairing those.
ADDED: Since the problem only occurs while you're moving, check that your new HU itself is well grounded. Many recent Subarus have a ground lead clipped onto a lug on the rear of the OEM HU. You can make a short wire with a similar male lug and a ring terminal at the far end, and attach that via one of the mounting screws on the side of the HU.
