It's doubtful that the power lead is the culprit.  It's most likely the
ground lead.  Try a new ground.  And yes, it's common for one amp to
exhibit alternator whine but not the other.  Some amps are more "prone" to
it.  Besides, the amp running your 6x9s will naturally be more sensitive
to it since it's not filtered out.

i have two separate amps hooked up, one for subs and one for 6x9's. the
smaller amp has its own ground, but the power and remote are off of the
other amp. the sub amp is running off of sub preouts, the other of of
the rear outs, not daisy chained. even when i used the high outs
instead of the rca's, it continued to pick up alternator whine, the
other never has. Do i just need to create its own power lead or is the
small amp the problem? any hlep? thnx

what about a ground loop?  i've never experienced this i only know its
something to avoid, and you didn't mention that they were grounded at the
same spot.