Fishing, I still find myself uncertain of the meaning of your description of the connections. I think you are saying (correct me if I'm wrong) that what you WERE doing was:
1)Connecting the "red treble" banana plug of the cable to the red binding post of the high frequency part of the speaker.
2)Connecting the "black treble" banana plug of the cable to the black binding post of the low frequency part of the speaker.
3)Connecting the "red bass" banana plug of the cable to the red binding post of the low frequency part of the speaker.
4)Connecting the "black bass" banana plug of the cable to the black binding post of the high frequency part of the speaker.
In other words, you were interchanging the connections of the two black banana plugs at the speaker end of the cable.
If that is correct, like Dan (Drubin) I don't see how that would cause the bass to be fine for an hour or so, and then mostly disappear. JJ offered a clever theory, but looking at the description and photos of the Comet at the AQ site I don't see anything suggesting that the gauge of the treble wiring is extremely thin, which it would have to be for a resistance rise due to heating to become significant.
Regards,
-- Al
