I have the same problem with my alpine deck. I had the 7894 and I posted the same problem a few months back. Did you also change out your speakers and added another amp for it? If not, I think you're probably using the internal amp for the Alpine and the factory amp for the speakers. I think you posted about this "double-amping before also. The high powered deck sends a loud signal to your factory amp, which in turn amplifies that signal. What results is that even if the deck is at a low volume, the sound you hear from your speakers is double amplified. However, the sub pre-out on your deck is still sending a lower signal to the sub beacuse your deck volume is still at a lower level. That's why you can barely hear anything from the sub.
At first I could only turn up my volume up to 8 or 9 max. After directly connecting the speaker wires from my headunit to the speakers (bypassing the factory amp), everything sounds fine now. I can turn the volume up to 18 or 19 now.
Hope this helps. If you have any specific questions, PM me.