I am having an issue with making the ASIs of a homebrew race. I put a "Choose an ability to raise by 2" on the base race, and a "Choose an ability to raise by 1" on a subrace, but only the subrace ASI is appearing in the character builder. I only have "Hide in Sheet" ticked for both options, so I'm unsure where my issue is.

Think of it like a building where the race is the ground floor and the subrace is above it. If you have two features with the same name the one on top will always superimpose itself onto the one below. So, because you have one feature called "Ability Score Increase” on the base race, and one on the Subrace, you will only ever see the one for the subrace in the builder. Your options are:

• Instead of making it a subrace, make it a very increase and have the variant races ASI feature replace the base race teacher.
• Name it something different.
• Simply attach both abilities for increases to the subrace. You can even have the features listed on the description page as two separate features, but simply attach the modifiers both to the subrace feature.

Does that make sense? 

I was thinking putting both on the sub might fix the issue. I guess this only pops up as an issue when you try to have floating ASIs baseline instead of in the Origin Manager stuff.