I am assuming you are using PEP2 for the 9400 editor. If not, please course-correct me.

Make sure that the Building Blocks Component is not associated with an extender.

The Component list is on the left (click the component with the codes), the codes are in the middle, and the associated extender/IRPort is on the right.

You might also want to post the IR data for one of the functions you learned so we can confirm if is a clean learn, etc.

Thanks in advance,
Lyndel