If I try to fade to back, I get no sound. It's weird but Bose only has two line inputs (not four) for the Audi TT coupe.

If that's true, then how is your empeg connected to this amp?

You're not making any sense. You say there are only two connections, but you were successfully using four connections before? How can a software upgrade change the number of plugs on the amp?

From what you're saying, you're correctly doing this, using just the front outputs plugged into the two Bose amp inputs, and leaving the rear outputs disconnected.

Assuming that the Bose amp is doing what you say it does (drives four speakers from two line inputs), then in this configuration, getting silence when fading to back is the correct expected behavior.

In that configuration, you should not be trying to use the four-way equalizer anyhow. Because if you do, you're wasting bands... ten of them never get heard. At least if you put it in proper 2-channel mode, you'll at least get more bands to provide more detailed control over your sound.

There is another idea, which is that maybe the Bose amp drives only two of the four speakers, and depends on the stereo's built-in amp to drive the other two. But the empeg never had a built-in amp like other aftermarket stereos. So the software change doesn't affect this situation either.

Still doesn't answer the question of why four-channel mode won't "stick" on your player. Even if the back two outputs are disconnected, it should let you select four channel mode. Perhaps it's just a user-interface problem? They changed the user interface so that you do things a little differently. Maybe you're putting the cursor on four-channel but you're not actually selecting/confirming it and saving that setting. Make sure you hit the "down" button on that option.

But from what you say, you shouldn't be using 4-channel mode anyway. Wasting bands.