Farmer NPCs not putting harvested crops in storage

Have you checked the crops are listed in the config notecard. You need to list all the items you wish to be collected (and you do need to get the upper/lower case right)  Also the farmer won't collect any crops that appear with the auto-harvest turned on, instead the farmer must harvest them first:
etc

If the above doesn't help, is the farmer collecting items but not storing them?

Ahhhh...I did not understand that you shouldn't have Autoharvest selected. I believe that was/is the issue. So...Autowater okay, Autoharvest not okay if the NPC farmer is going to put the crops in storage.

Thank you once again, Cnayl!

Yes, NPC Farmers are not the brightest of soles and can't 'see' any harvested items, they only put into storage the things they collect from ripe plants.

Update: 
- Unchecked Autoharvest on all of the crops / trees.
- Crops complete growing cycle and then restart to New.
- I can't see any evidence the harvested crops ended up in storage anywhere.
- Additionally, is it possible that occasionally the crop itself or farmer will "drop" a basket in place? I've noticed on fields with Autoharvest turned off, every once in awhile a basket appears above that field. Could still be user error on this one.  

Sometimes the farmer does manage to lose an item it is carrying, so that may be one thing.  For the crops, you can try adding manure to a crop that is at the 'growing' stage and that should move it to almost ready to be ripe, so keep an eye on it for 5-10 minutes and see if it produces any thing and/or gives any error message (you will need to stand next to it)

You can also try editing the item and in the description change the word Growing to Ripe and then reset the scripts and that will force it to be ripe straight away, so again you can see what happens.

Thank you. I suspect it might be a combination of things. I did as you suggested by both editing the description as well as adding manure and watching. both times, it looks like the farmer harvested and deposited in the containers correctly. I'll keep an eye on things but I also think there might be sometimes things disappear. Not a big deal, more curiosity. Thanks again!