Not sure if this is intended or not (I'm on ATLauncher's DNS Techpach) but MFR Fertilizer is not recognizing Agricraft crops. Is this intended, or...?
Bonemeal effects on crops is configurable. Might want to check the config and see if it's possible. I've noticed some methods of acceleration don't properly recognize crops, but that compatibility has come along pretty quick once noted to the dev..