The bug:
I am not exactly sure what could cause this bug, but their seems to be a bug with beacon blocks.
It affects only one of my worlds, I use no mods/texture packs. So I laid down a pyramid of diamond blocks(I have tried this with iron,gold,diamond,and lapis) and then laid down my beacon block, I opened the GUI and put one diamond ingot in, and nothing. It appears to not realize that their is a pyramid under it. The beacon works on all my worlds except this world. I have tried force updating. I have spent some time online trying to find similar cases, with no luck. I am sorry about any bad grammar/spelling, but my natural language is not english.
Edit: I do not have any solid blocks above it. Their is some water 20 blocks above it, but that is not considered a solid block, is it?