Please visit the Bandra office for the professional tax at GST bhavan, BKC, If your office is at Mumbai suburbs, check your Professional tax officer , and meet them, they will resolve this query, as there is change in rule ,while doing payment you have to select next month period instead of wage month. this querry will be solved by professional tax office only. take laptop and your payment challans along with you.
On January 2019 i was ipload all the pending PTRC return since april 18 to January 19 they have not charge any penalty or interest.so how much they charge in June 2019 , that you have to ask professional tax officer only.
As per law late filling fees is Rs. 1000/- per month, may be if you request them and give the letter etc they may waive the late fees.