Thats changing actually.
Due to the fucktardedly huge levels license costs were reaching (though guess what that money went to? And the money you pay for anime DVDs lets the companies license more, which involves SENDING THE JAPANESE COMPANIES MONEY, which results in more anime, etc etc) anyway, they are moving to systems where instead of an upfront lump payment, the Japanese company gets a percentage of the profits, which is somewhat riskier, but can also lead to more profit in the long run.
Not to mention, for shows like Haruhi, Lucky Star, FMPTSR and a few others, they are technically "licensd" by the Japanese company, and they hired US companies (Bandai, Funimation) to do the production work, but the profits go to the Japanese company, since they own the license.
Not to mention that Bandai Entertainment, as a subsidiary of Bandai-Namco USA is, ultimately, a part of Bandai-Namco Japan as well.