Problems with auxiliary audio after iOS6

I have a weird issue that doesn't seem to be addressed on any other threads. Hopefully someone can help.
My wife had a 3GS and she listened to music (mostly Spotify) through her car stereo via an auxiliary cable. This worked fine until she updated the phone to iOS6 late last year, at which point music would no longer play through the car's left speaker, only the right.
The problem wasn't with the car or the cable, because I have a 4S, also updated to iOS6, which played (and still plays) just fine through both speakers using the same auxiliary cable.
What makes it stranger is that I got my wife an iPhone 5 for Christmas. She still has the same issue that she had with the 3GS - no sound through the left speaker of the car. But plug in my 4S, and everything works just fine.
I'm lost. Any ideas out there or similar problems?

Possible solution here...
I have an aggregate of two interfaces with 16 channels. I can address now all inputs an outputs, but the slave interface doesn't meter anything and i don't hear anyting on the outputs routed to the slave interface. Also some debug output is printk'ed:
AM824NuDCLRead::Start() failed: 0xe0008020
   Finally, after a night long research, it is working as proposed.
My setup now en detail:
Mac Book Pro 2,4Ghz/3GB RAM/OSX 10.5.4
2 lynx aurora 8 / LTFW
1 Lynx / Internal Clock
2 Lynx /External Clock (via 75 ohm cable)
Uplink of the devices with a gold fw cable.
Link to the 1394a port via gold cable to the mac book.
I use an aggrgate of two devices 16/IN 16/OUT.
Problem was:
No sound on the slave Interface.
Problems that i found out:
Never run pppd via WLAN in the background.
A crosseffect letting the Systems Panel die and the devices are not accessbible.
After turning off wlan (dectivate) the interfaces are accessible again.
A weird crosseffect i mean.
Problem in the Audio-Midi Setup -> aggregate device:
BE SURE TO SELECT THE MASTER INTERFACE AT FIRST, OTHERWISE THE PLIST FILE IS WRONG, SINCE THE CLOCK HAS ALSWAYS ID 0 IN THE PLIST FILE.
IF SELECTING THE SLAVE FIRST  AND THEN SELECT THE MASTER CLOCK, THE PLIST FILE IS WRONG. CAUSE THE MASTER CLOCK IS THE SLAVE AND HAS ID 1 , WHICH IS ACTUALLY WRONG.
Hidden File with aggr. config: /Library/Preferences/.GlobalPreferences.plist
To view copy the file in your home dir in the console like: cp  /Library/Preferences/.GlobalPreferences.plist ~/test.plist.
Open the property list editor and select Your home directory.
View the properties.
SO, SELECT THE FIRST DEVICE AS MASTER CLOCK AND THEN THE RIGHT INTERFACE HAS ID 0. THEN SELECT THE SECOND ONE.
NO TROUBLES IN THE KERNEL ANYMORE. NO ATCP TIMEOUTS:-))
This solutions works for me now.
http://www.lynxstudio.com/forum/forum_posts.asp?TID=2250&title=two-aurora8-with- logic-8

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