So I just installed my 6000nex in my 2007 Toyota 4Runner, I'm a fairly tech savvy person I am a Cable Technition and also build computers as a hobby.  I wired my entire unit myself in my car.  6000Nex 2 amps 1 for sub 1 4 channel for front and rear speakers, all sound coming directly off front and rear RCA out from the Nex to 4 channel amp RCA in's,  and sub RCA's from Nex  to Sub amp RCA in.  The System BUMPS it sounds awesome, only one problem. 

None of the "command" audio is working at all.  I've done the update for carplay successfully I've tested over Bluetooth and connected with two separate iphone's a 5s running the latest ios and iphone 5 running the next to last version.  both Bluetooth or connected I cannot get any audio from Siri, incoming ringtone, on a phone call, the person on the other end can hear me, I hear nothing, navigation turn by turn directions. nothing, just dead silence when I try to use siri or any of these functions.  I'm not sure what's wrong, does the audio for this not run through the RCA connection of the 6000Nex? I'm at a loss, I've double checked every setting on the system, and iphone, and can't find any information online or in this forum about this issue.  I'm planning to call Pioneer in the morning but thought I'd check here first.  any help would be appreciated thank you.

Just updated to IOS 8.1 and updated HU Firmware to 1.08.  Still nothing... Going to double check my amps gain and frequency configuration tomorrow to see if anyhow that has anything to do with no audio from the "updates" not sure why it would but that's my last thought unless I have a bad headunit.

A few of us are having essentially identical problems with the 4000nex. We've tried everything you did and nothing fixed it. There's a thread on here about it that you should check out. One of us has sent his unit in for repair, and we're waiting to see what pioneer says.

Never mind, guess you found it! Just saw your reply on there.

Yea sorry I did just find it, I'm going to mess with it today, if I can't find a fix I'm yanking it out and sending it back while I still have my 30 day return on amazon for another unit.

So an update. On my system I have a 4ch amp supplying sound to all my speakers. Rca from and rear out from nex HU to rca in on 4ch amp. My amp is a kicker amp that has a "fader" button. With that button not pressed in i would not get phone or "command" audio with it pressed in voila, sound has returned. This fader button I believe has something to do with differentiating front and rear sound not sure. But that fixed my problem. Now to fix this intermittent popping... Hoping it's not a Headunit issue