It isn't just ducts, though. Some MFR machines seem to fail on unload/reload of chunks too. Though I suppose that could be because of a stuffed output somewhere along the line, though the machines appear completely dead as the "heartbeat/work" bar doesn't move at all.
As far as ducts go it is kind of funny considering I switched away from Buildcraft transport to Thermal Expansion transport specifically because of how TE's just seemed to magically work across multiple chunks without issue in 1.4x/1.5x. 1.6 has seen me go back to BC in packs where I have the option. I've managed to corrupt a save in practically every 1.6.x pack I've played, thanks to Thermal Expansion.
That is exactly due to either a stuffed duct or a 'no longer valid' inventory.