Tom,

If your speaker swap didn't fix it (it probably didn't) I can take a pretty good guess what is causing it.

You are most likely gettting destructive interference between the sub and the right speaker.

Unless your room is perfectly symetrical, your listening position is exactly in the middle and the main speakers are the same distance from the front and side walls AND the sub is in the center this can/will happen in at least some frequencies.

A way to start understanding how bass interacts with the room and multiple speakers is to take the meter and play some tones while slowly moving/walking around. These dips and peaks you'll see are called "nulls" and "peaks" are areas where the sub freq have destructive and contructive interference with themselves.

If you have two subs, you can place one on each side symetrically and you would no longer see one speaker having a drop in the xover area. Also try moving you listening position or sub, left/right/forward/back to find an area that is at the midpoint of both interactions.

Hope this helps!