I seem to have fixed my problem.
1. Power your Modminer Quad (MMQ) via molex, but don't plug into computer via usb.
2. Reset MMQ by bridging left-most two contacts on the RESET pad with a conductor for ~5 sec. See instructions here:
https://www.modminerquad.com/index.php?title=Firmware (note: I did not touch the ISP pad)
3. Plug MMQ into computer via USB. Verify drivers are correct, should be "ModMiner QUAD" not "ModMiner LJRalpha". I used drivers from
https://www.modminerquad.com/index.php?title=64x_Windows_Drivers. Don't use these unless you are 64bit.
4. Start bfgminer. It recognizes the MMQ and decides to upload a new bitstream.
This worked for me. I'm not sure how it all got messed up. I tried powering my 2 MMQ from a new ATX power supply today that wasn't connected to a motherboard - perhaps this spiked the power and corrupted the FPGAs. In any case, resetting seemed to do the trick - now my MMQs are getting about 830 Mhs.
Good luck