If I'm not mistaken, you can register with the same name/username. But the two worlds are separate areas, though the web site may seem to provide an integrated experience. From a community account alone, Qlik cannot deduce whether you are an employee, a partner, a customer or neither.
BTW this could be a sign of an intermittent problem that occasionally occurs in the Partner Portal as well. After a few hours/days, the problem is fixed/goes away. If you are sure that it has nothing to do with accounts (i.e. it worked before with a single account) and the problem doesn't disappear after a few days, I would suggest to contact Qlik Support.