As the OP pointed out, there is a sound difference between the AUX/iPod/Radio and DVD media sources in the car. The difference is most noticeable on the DVD Source. There isn't anything I know that can correct it, but I can assure you it's more noticeable in Logic 7 systems. Yes if you would like to use 5.1, you need to enable the Logic 7 (tested). If you are not using Dolby Digital 5.1 or DTS 5.1, you might have issues.
Model: 2009 E92 | Color - Mojave
Made: February '09 - Germany | Interior - Beige Dakota/Gray Popular Trim
Current Country - USA | Mileage: 66699
Options: Navigation/Premium/Cold Weather/Heated Steering Wheel/Sport Package/Staggered 19's/Rear Sun Shade/Park Distance Control/Comfort Access
Victims: Audi A6, Mustang GT, Cadillac CTS, Chevy Camaro, Porsche Carrera GT2, Jaguar XKS
Top Speed: 173mph