Hmm I personally dont know anything about BL4000 but I suspect that it might be the ipod -> line in-cable. With my moderate knowledge of sound I think that headphones out and line in connection differs abit (i suspect that you use the line-in connection on BL4000).
I would test the speakers on a "true" line-out (on a amp) to see if you get same behaviour.
Hope you are able to get it all working
Cheers
Jesper
Sweden