If the harvester can't see an output path to a valid inventory, it stops scanning its area for mature crops.
Not sure why that should happen when you have a chest on the output. Maybe try something that isn't an enderchest? All i can think is it may be a cross-mod compatability thing.
EnderIO item conduits are good, btw. If you whack a bundle with a yeta wrench it will give you a readout of where the items are being routed to. I tend to route into a tesseract for this sort of thing. Either that or an ME interface on the output works too, since you seem to have a network underway (but not an import bus, harvesters don't see that as a valid output for some reason).
EDIT: also I may be wrong but in the second picture it looks like you have an itemduct set to input on a harvester. That won't show as a valid output either, for obvious reasons