I've found that ME/NEI-synchronized auto-search is less likely to function the busier the ME network is. It appears to be a low-priority process controlled by AE, so that when a lot of crafting and/or exporting/importing is going on, it will be considerably delayed to the point of being completely nonfunctional.
So if it works once and not anymore after that, can it be you have submitted a big crafting request? Ore coming in fast from an auto-mining facility also count.
Also, before you restart FTB, try breaking and replacing the ME Controller. That has always worked for me so far in cases where the system refused to do anything.
