Some pics would help alot! Sounds like you could have a pH/nutelock issue. Have you checked the pH of the runoff? It should be in the mid to upper six range for soil.

Rootbound is definitely possible with 2 gal pots. I would check that asap. Also, rainwater is usually not a good idea unless it tests ok everytime. It can contain all sorts of nasties, and its very variable in quality.