Figured out my Scrypt-N issue.
Turns out "--nfactor 11" no longer works with waffle. It's been months since I've updated my scrypt-n configs so I never changed it to the newer SGMiner scrypt-n parameters.
Very odd, since it's been running solid for weeks without a restart using the old params and was still up and running two days ago. It only exhibited 100% rejects after I had to reboot the box.
Switching to this conf setting fixed it:
"algorithm":"adaptive-n-factor",