Matt, if I understand correctly you're plugging the 2nd symbilink into the amp, but you're still only getting signal from one of the symbilinks?
I don't have the DC Reference Amps, but I do have a regular Reference 1000.4. If the fader from the EQ isn't working, assuming the amps to the speakers and symbilinks are wired right, chances are there's a source setting on or in the amp that you haven't changed. I can tell you on the regular Reference 1000.4, if I went from a one symbilink input to a two symbilink input, like it sounds you are trying, there is a button I would have to push for the amp to draw from two seperate symbilink inputs verses the one you were using. Now I'm not sure on the DC series if this would be a button on the outside of the amp or something that may need to be done via a computer (I know the DC series can be digitally tuned and adjustments can be made from a PC), but you should be able to find that out from the manual for the amp. Or if you don't see any buttons on the outside of the amp, that look like they have something to do with a source, chances are it may need to be done digitally.
Another thing to check and make sure is the jumpers on the respective symbilinks. I'd start with them at 0dB, not sure what they were installed with, if you look at the symbilink itself you should be able to figure the jumper part out.