Not sure that it's the software at fault here, as the first place I installed my Empeg was an Audi TT 225 with Bose, and never had any problems regardless of which Empeg software version I was running. At the time, I used an Autoleads PC9-404 adapter to connect into the Bose system. It did need two pins moving around (front l/r moved rear l/r positions, I think), but it worked flawlessly.

You might want to check your install against the pinouts below, just to make sure you've got everything wired up okay:

BOSE Pinouts

Multi - pin connector I, 20 - pin
1- Line out, rear left
2- Line out, rear right
3- Audio frequency Ground
4- Line out, front left
5- Line out, front right
6- Switched positive supply
8- Clock signal for radio frequency display on instrument cluster
9- Data signal for radio frequency display on instrument cluster
10- Enable signal for radio frequency display on instrument cluster
11- Remote control (steering wheel)
13- Data - in signal for CD display on instrument cluster
14- Data - out signal for CD display on instrument cluster
15- Clock signal for CD display on instrument cluster
16- Permanent positive connection
17- Switched positive supply for CD changer
18- Ground connection for CD changer (CD audio frequencies, Ground)
19- Signal wire for left channel (CD audio frequencies, left)
20- Signal wire for right channel (CD audio frequencies, right)

Multi - pin connector II, 8 - pin, brown
3- Loudspeaker (+) front right
4- Loudspeaker (-) front right
5- Loudspeaker (+) front left
6- Loudspeaker (-) front left

Multi - pin connector III, 8 - pin, black
1- GALA (road speed signal)
2- Telephone muting
3- K diagnostic
4- Connection for switching on and off via ignition key (S contact),
terminal 86s
5- Switched positive supply for power antenna
6- Switch illumination (terminal 58s)
7- Terminal 308- Ground (terminal 31)

Multi - pin connector IV, 10 - pin, red
1- Telephone muting
2- Terminal 15 (only on vehicles with navigation system)
3- Telephone (audio frequency +)
4- Telephone (audio frequency -)
5- Navigation system (audio frequency +)
6- Navigation system (audio frequency -)
7- Navigation system control wire
9- Display illumination (terminal 58d)
10- CD Ground (CD GND)

If I can find a copy of 1.13, I'll PM you.

Bagpuss.