I found this bug from two years ago that was fixed, but it seems to be back.
At Level 5 and Level 8, when I select “Upgrade Subclass,” there are no options to get the extra 1 companion skill (Level 5) or 2 companion skills (Level 8) in the character builder.
Sorry about that, I was at GenCon and I’m only now getting back to it. I’ve got a ticket filed on this and we’ll take a look at exactly what’s going on!