I just connected the subwoofer multichannel output line directly to my sub from the oppo and it did receive signal. The problem has to be either the way I have the 990 set up or a maybe a defect in the 990.
Gonk is more experienced in this than I, but if you get a signal going directly from the Oppo to the sub, and no signal through the 990, I'd look for a problem in the 990.
You might want to particularly check you crossover settings on the 990( you may even want to jack them all up to 80 or even 100 for the sake of the test), make sure your speakers are all set to "small"on the 990 and make sure your speakers are all set to "large" on the Oppo.
As gonk recommended, a test disc is a good way to verify what's happening. (I use the Avia disc for such things).
If you still get no signal from the 990 to the sub, you might want to call tech support.
Do you get bass to the subwoofer from other sources ?