That is unfortunate to hear - I have had amazing results with the 622C system under various conditions. At the suggestion of the dlink below, I have been using Alkaline batteries rather than NiHM rechargeables as the voltage drop-off is sudden on NiMH and with Alkalines it is gradual. The 622C's require 2.2v to operate correctly.
Is it possible you are up against a similar design constraint with the YN-E3-RT? Perhaps try a good set of Alkalines in them instead.https://docs.google.com/file/d/0B77OmmGIg0gMVFpqNkpBYXBHajA/edit?pli=1
A couple of quotes from the link above...
"If the voltage becomes low (total 2.2 volts), the 622 will turn off automatically."
"Alkaline batteries start at 1.5 volts and hold their voltage until the very end. Rechargeables at 1.2 volts are already 20% down, and approaching the threshold for the 622. Alkaline characteristics are well suited to this type of device, with a 60-hour standby time. (NiMH batteries are great as flash batteries, being capable of a rapid discharge into the capacitor.)"