Could have been the sub, no way to tell for sure.
If that is the whole sub plate you posted, I don't see a control for crossover frequency. I don't see a low pass switch either. Those may have given you the ability to make the sub more pleasing to your ears.
Just guessing, your only options were to use the sub volume, and the Luxman bass/loudness (if equipped) which would have affected the bass of your main speakers.
A newer receiver/amp might have a function to set the cut off frequency going to a sub.
That sub did have a phase switch, it should be fairly noticeable when changing from 0 to 180.
Maybe, if you get the chance, try another sub. If you could borrow one that would be best since you already tried one and didn't like it not sure I'd recommend spending money on another one.