We are not adding the same user ID with different business partners in SRM. User 1 and User 2 will have different ID's but are the same person. I think that is what is confusing the SRM org structure side. User 1 and User 2 will have unique ID's, position numbers, and employee ID #'s. But, because they have the same home address, the SRM org structure side thinks they are one and the same.
Everyone is in the same country/company code.