Yes I did.
Turns out, from what I've read, that if one or more energy conduits is chunkloaded and the rest aren't, it causes issues. I recently hooked up a quarry through tesseracts and energy conduits. However, I completely removed the offending quarry, energy conduits, and tesseract with no success.
EDIT: When I re-open the world in MCEdit, the blocked that were removed are immediately returned. :I What the hell?