Source: Anime News Network

On March 24, TV Tokyo and Nihon Ad Systems filed a joint lawsuit against North American media distributor 4Kids Entertainment,
accusing the company of "underpayments, wrongful deductions, and unmet
obligations" and stating that 4Kids now owes the companies
US$4,792,460.36. The Hollywood Reporter website also states that the two companies have terminated their deal with 4Kids.

According to the documents filed by the plaintiffs, the companies conducted an audit on 4Kids' Yu-Gi-Oh!
business per their licensing agreement. This audit allegedly uncovered
the aforementioned underpayments, as well as a "secret" agreement with Funimation, allowing them to "exploit" the Yu-Gi-Oh! franchise via home video and hide the added income from the plaintiffs. By hiding this income, TV Tokyo
and Nihon Ad Systems allege that 4Kids was able to pay them a smaller
share than would otherwise have been owed to them. The complaint
further alleges that 4Kids attempted to hide the secret deal rather
than disclosing it as required by their licensing agreement.

Funimation is not listed as a defendant in the complaint.

More in the link.

Well this a serious blow to 4 KIDS as Yu-Gi-Oh! was their last Bread & Butter, though I am interested as to why Funimation is in the clear when they are mentioned as being part of a "secret agreement?"