Check the guage of the wire which is running from the battery negative(-) to the frame of the car. I had some alternator whine which turned out to be a small (14Ga) guage piece of wire grounding the battery to the frame. If you are drawing 40A through a 4Ga wire on the positive(+) side, no problem; but you must provide an equal current capacity on the negative(-) side. A piece of 14Ga wire won't get it (well, for long anyway). What you are looking to do is provide a current path with the smallest amount of IR drop from one end to the other. I still have a small amount of alternator whine; however, I only notice it when I've got it cranked up during a soft passage. Here's what I ended up doing:

  (+)---4Ga---FUSE---4Ga---(+)
Battery                    Amp
  (-)                      (-)
   |                        |
  4Ga                      4Ga
   |                        |
 Frame                    Frame

It's worth, at least, checking the gauge of wire which is connecting your battery to the frame. Especially since you mentioned running two amps fused for a total of 45 amps (20 and 25); the return path should be able to handle 45 amps.