Hmmm, this issue has not been reported before. It might just be a gameplay issue.
I had a quick look into the code. SUB3 is not required for Gwynn to use the milking machine. Once you have built the machine, you can ask Gwynn to "test it out". In that cutscene she will get SUB 3 afterwards. So I assume you did not do that part with Gwynn yet.
If you play the game without mod you can send me a link to your a relevant save game file and I'll have a look.