Apparently PCB had requested to submit the visa applications first, and then submit the passports to the Indian high commission after the team's return from Sri Lanka, as obviously the passports were required for the team to travel back to Pakistan. But this request was denied, and the applications along with the passports were submitted after the team returned from the Asia Cup, at the start of last week.
Bangladesh and Sri Lanka have yet to announce a squad, but their visas have already been cleared, as Cricinfo is reporting that only Pakistan's visas are pending.