Modpack version Enigmatica6-0.5.4

Describe the bug
If you use building gadgets to build the whole structure (like I did) it appears to futz with the apiary and causes it to only output combs. If you break the apiary and replace it, the bees will start to output blocks.
Created this on the public E6 server, was able to duplicate it in SP world.
If it's an issue on the building gadget side, or if you think it is, I can link this over there.

Logs
This is the building gadget paste.
https://pastebin.com/cBfawvyk

Screenshots
n/a

This isn't super surprising; Building Gadgets frequently doesn't play nicely with tile entities. I would recommend making your schematics without the apiary block (and likely storage and breeders), and place those by hand last.

Yes please to linking it on Building Gadget's issue tracker :)