My guess? One woofer or VC is wired out of phase. Sorry if this isn't it, or if it's insulting, but I'm a fan of trying simple solutions first.
Try hooking up a 9V battery to each enclosure at the speaker wire. To check the two woofers within an enclosure, doesn't matter which way the batt's hooked up, but the woofers should move the same way, both out of box, or both into box. Because they're DVC, it's even possible one woofer might be hooked up not to move under power, which the amp probably wouldn't like. The choice of a 60Hz frequency was problematic, because there's actually enough of a phase difference at 60Hz that you'll get some output with one type of wrong hookup. DC should solve that problem... So the guess is that one woofer is hooked up to move the wrong way, or not at all.
Also, the multimeter tells you the woofers are hooked up, yes, but not necessarily the right way.