I can't buy anything from the shopkeeper IF the price is ABOVE one stack of emeralds.

And some of the stuff they are selling i`s REALLY great so you want it! :)

LOL, yes that was a bit of a goof. This bug is reported here:

Unable to buy expensive items from shopkeeper due to emerald stack limit #112

Thanks for letting us know though! For now you need to work on getting your rep higher so that the prices get cheaper or use the Villager Market as a work around suggested by @Zygus42