Tim, I have the Pioneer SC-99 and I am having the exact same problem not only with my IOS 9.3.1 devices, but also with 10.12.2 of MacOS. I have read from other posts that the problem seems to be specific to AirPlay on 5 GHz wireless, and not limited to Pioneer devices:
AirPlay mirroring is broken on 5ghz Wireless band
My new Apple TV v4 does not work smoothly on Airplay with both my MacbookPro and Air laptops but fine with iPhone and iP…
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I have a mac mini with 10.12.1 on it which happens to be wired and I never have had problems with it. I am about to test iTunes running on my 10.12.2 MacBook which glitches when on 5 GHz and put it on the wire to use AirPlay to connect to my SC-99 which is already on the wire and I'll report back if I continue to have problems, but my money is on the problem will vanish under these conditions.
I guess the other wireless solution would be to run on 2.4 if you want to play music from a wireless device, which would really be a shame for me after spending $250 on a multiband 5 GHz Router/AP. If I were to called Apple support, I pretty much expect that they will blame Pioneer for this problem so I am not going to waste my time unless I can grab an old AppleTV to replicate the problem. Honestly, I wouldn't be a surprised if it was another Bonjour issue.