I do not know the real reason but many companies retain a portion of End of Service Benefits/salary for the Notice Period for some time and remit to the ex-employee's account in due course.

If you work for a good company (you should know that after having worked for 2 years with them), do not worry, they will remit your dues to you. But if you doubt, claim and settle it before you give your passport for visa cancellation. While you are here, they can't cancel your visa without submitting your passport to the authorities. You have some leverage.