When re-loading a chunk with a comparator on a corporea crystal cube, sometimes the comparator will not output a signal even if there are items in the network.

Just FYI, this sounds like an earlier duplicate of #3763. It's fixed for 1.16+ by f60aa3d.

just out of curiosity, are there any "chickenchunks chunkloader" present? They act funny sometimes!

nope, no chunkloaders of any kind