could be a problem with the AVIC, or it could be a problem with the BOSE integration module, or it could be a problem with the bose amp itself, i have seen all of the above. you will have to trouble shoot to identify which component is to blame.
temporary put the factory radio back in, if the problem goes away the the bose amp is fine
most of the bose integration modules has RCA inputs to get signal to the amp, hook up a MP3 player directly to the RCA connectors with a mini to RCA cable, if the problem goes away the the module is fine.
in my experience, the modules seem to be the most common cause of problems.