How can I make my farmer villager replant crops? (1.8)

Throw them two more stacks and try again.

According to the "Villager" page on the wiki they will pick up 8 stacks before their inventory is full, not 6:

The villagers will pick up 8 stacks of items before their “inventory” is full.

After their inventories are full they will stop picking it up:

After their “inventories” have been filled up, they will continue to tend to crops, but will not pick up anything they collect.

You should also make sure that you have chosen farmer villagers to do the work. It will not go down well if you have chosen a butcher or a librarian to do the farming work. Make sure you farmer villagers they look like this:

Also, in 1.9 and above, right clicking (trading) with the villager will tell you the profession. This is important because there are other villagers with plain brown robes now.

I had the same problem. Same set up with the mine cart running under the farm.

I have a Village with about 50 Villagers. It seemed the only thing my farmer wanted to do was get to the other Villagers or get to the center point in the Village. I moved the Farm about 50 blocks from the Village and he now farms.

I put 8 stacks of seeds on a farmer/fisherman/shepherd or fletcher,(any villager with a solid brown robe). I only did Wheat because it's the only one that seems to work with the mine cart under the farm.

Carrots and Potatoes seem to work a little differently with the farmers. If you fill the farmers with 8 stacks of carrots or potatoes they wont pick up anything. But they will place it. So I use water to push the items to a hopper for the carrots and potatoes. The farmer will replant after the flush.