I'm having the same anoying thng happen to me and my iPhone 5... This started after the most recent upgrade to 6.0.2 and only when on my Apple USB cable to my PC
Your all trying to find technical solutions to a simple problem.
The problem is the CHARGER, not soft ware updates etc or phone settings but the charger.
Simple to prove.
Firstly the phone always beeps when you plug in the charger, but then keeps beeping, the reason is that the charger switches off and then on again, hence the second beep and also whay it turns its self on again.
To prove this change the charger. Also when you plug it in you notice the battery symbol shows a flash to show it is charging, then if you keeping looking at it the flash dissapears, ie the charger is not on. then it switches back on again. lets face it what do you expect from a mass produced made in china charger produced in the millions.
I went to the apple strore and they gave me a new charger NO MORE BEEPING NOW.
What you will find is the apple store is full of techo geeks trying to impress you with technical solutions to simple problems.
Sorry I m old school, break problems down into sections and prove each section, but that is what happens when you were a telephone exchange technician taught in the time honoured KISS manner.
Keep It Simple Stupid
Go get your selves new chargers and dont worry about software update 6.02/////#$??? and you will spend time using your phone