This issue is happening on Recurrent Complex 1.4.8.2 on Minecraft version 1.12.2 with forge-14.23.5.2847. I noticed it first on All The Mods 3 Remix, but I've reduced everything down to a small number of QOL mods and it's still happening.

Essentially, I'm trying to get a structure to generate in towns. The structure can't be rotated (because EnderIO conduits misbehave when rotated), and it has a single exit on the North side. When I specify that a structure can't rotate and has an exit on a fixed side, it never (or almost never) generates in villages. When I either allow rotation or exits on all sides, it generates just fine.

Steps to replicate:

1. Download the zip file from https://complex.ivorius.de/submissions/99 and put the structures in your active folder.
2. Set up a vanilla forge instance with Recurrent Complex.
3. Disable generation of Recurrent Complex's built-in structures (it's reproducible with them enabled, but I'm aiming for a minimal test case)
4. Create a superflat world (I did one bedrock, 62 dirt, and one grass)
5. Fly around in creative mode and check all the villages. Note that green and blue arrows generate, but red arrows and my custom structure (with the ender i/o stuff removed) do not generate.

Note that the green arrows do not rotate but allow exits on all sides, and the blue arrows rotate but have the exit set to north. Both of these generate and behave as expected.

Here's a screenshot of a typical village from the test case:

https://imgur.com/a/GTHM2WQ

This usually happens because when you set a structure to only have one possible rotation, this limits the possible places it could generate in the village, making it naturally rarer. You could try bumping the weight up (in case you haven't fixed it already).