I'm playing with the Enable All Planets Mods, which means I have a jillion mods installed, but after this got added, suddenly, Metal and Stars' Overclock Module stopped working, as in, the game says you aren't allowed to install these modules in any machines they're supposed to go into. I eventually found that the indexing option in Startup settings in this mod fixes it, so you know.

If the startup setting fixes the problem without creating any additional problems, then I'd say it's working as designed. In the next version of Voidcraft I'll change the defaults settings so that automatic module categories are enabled by default if you're using Enable All Planets.