OK, well after 1/2 a day of trying different things, I finally got it. Hopefully this helps someone in the future... Apparently the positioning of the head unit relative to the actual power meter units is extremely sensitive. I positioned the head unit like in the picture in the .pdf file from Pioneer which allowed me to successfully update the left side, but not the right side. This is how I had to position the unit to update the right side:

I sent my whole crankset in to Pioneer for dual side installation. I almost went with Precision 4iiii but they hadn't released the dual side to the public yet. Pioneer seemed to have good reviews and it's compatible with other head units. I didn't want to have to buy another head unit. It's working well as a dual but now I need to contact Pioneer and see what they can do to fix it so I can hopefully get the left side working independently. That was the main reason I got it. When I tried taking off the left arm and putting it on my TT bike but my Garmin 520 searches for it, but can't find it. The local distributor had the pioneer software. He updated the firmware but it didn't help. Re-installing batteries or holding the little button in for 3 seconds didn't change anything. Have you tried to use the Left arm separately?
Marty

I have not tried to use them independently and have no experience with that, sorry.

You sure am glad I happen to see your post. I was having the same issues updating the right side firmware. It was getting frustrating. I guess positioning is the key. I moved the head unit within 3-4 inches and had no further issue.
Yes, your post helped a lot!!

FYI, we're up to V 5.030 now on the actual power meter parts.

Just checking this thread to make sure problems are good? I have the PM dual and updated no issues.... If it is multiple users, I may follow up with Pioneer on the update issues, if any.

tks