I believe there is flawed logic in the trading station.

I have went to an empty area away from villages and randomly spawned a village that trades 1 emerald for 3 bread.

I then open the trading station gui and say I would be willing to trade 1 emerald for 2 bread.

This trade never completes, although I would expect it to as the villager would get a better deal (only paying 2 bread for 1 emerald) or since my deal is better than what is offered by the villager, the trade would auto complete and give me the 4 bread.

I then removed the removed the emerald from the trading block inventory, change the trade to 1 emerald for 5 bread. I then place the emerald back into the trading block inventory. I would expect this trade not to happen because I do not want anything less than 5 bread for 1 emerald, but the trade processes and I am only given 4 bread.

I am running 1.7.2 forge v1126 and railcraft v9.0

I also tried railcraft v9.1 and it appears the same happens

Yep, that's wrong. Fixed.