There are many factors that go into determining the output of any given building. Building level, size, % boost, etc. Not certain of your exact situation, but if the scroll building is of a higher level than your crystal building, it will produce more. Also, you will notice that not all goods buildings are the same size. For example, a 3x3 building will have a greater output than a 3x2 building. If you have all of those building at the same level, you will see that your boosted relic will give more per square than the others.
You will be able to increase your boost percentage through obtaining crystal relics from neighborly help, provinces, and tournaments. Hopefully you will soon see a much higher production of crystal.
I hope this helps!!