I would imagine they might still owe residuals to former employees and other companies that they had licensed 'intellectual property' from. Like they might be paying Amblin Entertainment for the exclusive rights to producing an ET video game. Or owe money to some developer that wrote some chunk of code that is still use with Atari's licensed properties.
But those things wouldn't account for the $22,500,000 hole in their budget... Even adding in the $3,300,000 in salaries, rent on an office, and other operating costs, there is still a lot of money missing.