The above is the answer, but I'll post this here for reference as well. I've noticed a few oddities with the FTBUtils chunkloading (others have mentioned similar things).
In my case, my farm system stopped working when I left the area. What's annoying is, I can't diagnose which mechanic isn't working without being there. My system is using Rotarycraft Fans to harvest a field, allowing me to harvest without having to replant. At the end of the field, drops are carried to a Hopper via a stream of water. The Hopper feeds into an EnderChest which is emptied at by warehouse.
From my experience thus far, I suspect the issue is the drops entering the Hopper from the water while I'm away. As soon as I come back into range to load the chunks, the Hopper is flooded with drops. My next test is to use a different item collection system (OpenBlocks Vacuum Hopper), then test other theories less sound until I can make it work.
As I stated above, others have had issues with chunks only being semi-loaded, but I've not seen any definitive data on what does/doesn't work or why. My first thought was that they used a loading similar to Spawn Chunk loading, which doesn't allow for crop growth unless a player is present, which is a theory I've not completely ruled out. More testing is needed.