Crimson Brews and Potions of Duty are the ones I've found to suffer from this, but probably other "unique" effect ones would suffer from this.
It gives the error message "JHOMOGENEITY: I'm afraid I can't do that. I have not learnt enough about these potions to assist you."
Character: Tomal Neves
GSID: Pigadig
Custom potions not homogenizing is completely normal, although it is unusual that you're not being told this outright.
Are we sure that HAL 9000 is not running things now? That sounded like the sort of response he would give. "I'm sorry Dave, I'm afraid I can't do that."
Just noticed Johannes' portrait. That's just creepy...