A cd player should work with the sub, Alan has mentioned doing this to check a sub before. The rest of you have pretty much covered it, well done. My first thought was as Peter mentioned some sort of dynamic compression is being used on the yamaha to keep the range low which would explain only the most extreme LFE making it to the sub.
I would also suggest calling Axiom to see what they say and any possible help/suggestions they may have, you may find a new amp on its way and the problem solved by this weekend.
