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I have a Kenwood 5140 and it's been running fine for about 6 month. I have the stock bose speakers and they've been working fine as well. However, a couple weeks ago, the bose subs cut out (no power to the amps?). The weird thing is they do come on if I am using the tuner. If I use a CD, DVD or Ipod, no subs.
I remember seeing something about this before but I can't find it now.
Are you absolutely sure they've been running fine for the last few months? Normally the problem you described is due to someone connecting the blue 'antenna remote' to the sub trigger instead of the blue/white 'amp remote'. But then the subs would have never powered up in the first place.
If everything is connected properly, the most likely possibility is a blown #28 BOSE fuse in the passenger footwell, or maybe a bad BOSE relay #45.
Yet another possibility is the the wires are connected wrong, but you somehow just recently changed the settings for the antenna wire to only come on when the radio is playing instead of always being on (if your HU can even do that ).
I agree that it seems to point to the wire, just don't understand if it was wired wrong, how it could have worked for six months. I'll still check the wire this weekend and let you know.