This is, as far as I’m aware, normal behavior for 0.99 from upstream - because the standard organs are hardcoded now, any attempts to edit them fail - they’re compiled with the game executable instead of being interpreted on-the-fly. The organs you’re loading in are the external .organ files, which are slower and may have compatibility issues with existing characters and scripts due to processing differently.
At the moment, editing standard organs generally requires either renaming the organ and telling a character template to load that organ in place of the standard one, or editing the source organ file (in src/fetishmaster/bio/organs/<OrganName>.java, if you’ve downloaded the source code) and recompiling the game.
At some point in the past I had it reversed so that it would look for the scripted .organ file first and fall back to the hardcoded ones only if an external file couldn’t be found, but I reverted it pretty quickly. Not only is it slower, but inevitably someone’s going to drop in organs from an older mod that might have performance issues or work in a manner that’s inconsistent with the newer game direction. Instead I’ve just been focusing on minimizing the need for external organ files - trying to keep compatibility with as many mods as possible while still adding features or trying to balance the code.