This is a rather strange kind of contract of employment you have mentioned.
If you are recruited on salary and have to follow terms and conditions which are like in case of a regular employee e.g. you have to tender/serve notice period, tender notice pay etc, you should be an employee of the company.
You have served notice period and you have been paid salary. However your commission is higher than your salary and that is what you want. Company is maintaining a studied silence.
Did you handover the charge and company property under proper acknowledgment?
It shall be appropriate to show all of your documents to a competent and experienced labor consultant/service lawyer and give inputs in person and proceed under expert advice.
If possible you may attach a copy. You may erase the names etc to maintain the confidentiality.
You may narrate all representations { date wise with name, designation, dept, address of the company personnel to whom you have represented in person, by email, by phone, letter etc and mention minutes of discussion} made by you so far, in writing by a letter preferably addressed to good offices of your appointing authority, MD, Company Secretary and demand your dues { provide details} acknowledgment/acceptance of resignation { enclose copy of notice and final resignation, and POD of both and mention name, designation, dept, address of the company personnel, who asked you to serve the notice period, and mention that you have served notice period as instructed in office and handed over the charge}, work experience/service certificate, relieving letter, correct FNF statement, FNF dues by Bank DD, form 16 as per correct FNF statement, PF number, PF account slips of all the years, NOC/NDC etc. by redg. post only. You may mention that a postage prepaid {as purchased from PO} self addressed envelope is enclosed herewith for sending the redg. post to you.
Await reply and submit reminder. If your matter is not resolved you may have to agitate in appropriate forum which may be o/o Labor commissioner, of civil court.