avic d2 in 06 toyota sequoia

I have put in an AVIC D2 in a 06 Toyota Sequoia with a JBL premium sound system. The problem I am having is the sound is very muted w/ video and the nav voice, but the CD plays great. I used the metra TOYO 01 wire harness to hook it up. It played fine for about 6 months, then all of the sudden this problem came up. I have swapped the head unit w/ same outcome. I checked the settings and the volumes are all the way up. When the factory amp turns on the front two speakers play then after a short delay the rear driver side then the rear passanger side comes on. Any suggestions? You all know that if it is the factory amp it will be my fault anyway!

Anyone? I need to get this fixed!

I would do a temp hook up of the radio into a friends car (no factory amps) and make sure that the problem is not with the head unit. Are there any adjustments on the harness? It is possible that the harness is screwy provided that it has adjustable levels. If the harness is fine, than you can begin the grieving factor for your factory amp.