The Terrors were poised to ask FIFA to investigate the matter after the Premier League outfit failed to produce the money on time, but the situation has now been resolved.
Hull commercial manager James Mooney insists that the delay was due to a technical error, with the money being sent to the wrong place.
"We sent the money to the wrong place," he told reporters. "It went to the Premier League rather than the FA."
Hull signed the Scotland international for £2.85m this summer, with the remainder of the fee due next year.
Another of his former clubs, Queens Park, will receive a 10% sell-on fee as part of the deal.