Transit custom Stereo volume problems!

[Stutchie]

Hi everyone.

Got the most annoying problem with my Transit custom.
Its a 2014 trend 125ps panel van with auto start/stop and all trend features.
The problem is with the volume on the factory fir stereo. I can be listening to the radio or to my Iphone plugged into the USB and all works great for 10-15 minutes then suddenly the volume will start fluctuating from low to really high and back to low, and continue like that for the rest of the journey. As you can imagine, its so annoying!! Was wondering if it could be the amplifier on the stereo or maybe the alternator is playing up? Its a duel battery system with Start/Stop so wondering if thats a potential issue if one of the batterys is knackered.
Birchwood Ford keep telling me its fine, but clearly its not.
Have a video clip but not sure I can upload it.
Any help or suggestions much appreciated.

Will