This is a known problem with enhanced premium audio in cars built before 4/08 - the amplifier doesn't have a fan and overheats, causing the sound to cut out and in some cases make a loud popping noise as if your windshield was hit with a rock. It is especially bad on hot days.
There is a TSB out on this and a fix under warranty. See below.
SI B65 24 08
Audio, Navigation, Monitors, Alarms, SRS December 2008
Audio System Is Intermittently Inoperative
E90 *(M3 Sedan)
E92 *(M3 Coupe)
E93 *(M3 Convertible)
E60 *(M5 Sedan)
*with option 752 (INDIVIDUAL AUDIO SYSTEM)
Vehicles produced up to March 2008
Intermittently, the audio system is inoperative.
The amplifier for the M Individual Audio System overheats and turns off. The affected amplifiers are not equipped with a cooling fan.
Install an improved amplifier (including a cooling fan) for the M Individual Audio System.
65 12 7 842 409
Amplifier for M Individual Audio System
Covered under the terms of the BMW New Vehicle Limited Warranty.
65 12 31 42 00
65 12 072*
Refer to KSD
Removing and installing amplifier
*Main Work - use this labor operation number when this is the only repair being performed, or if this is the main repair when performed along with other repairs at the same time. If this is not the main repair, refer to KSD for the associated (+) labor operation code.