All perfect praise be to Allaah, The Lord of the Worlds. I testify that there is none worthy of worship except Allaah, and that Muhammad is His slave and Messenger.
1) Apparently the 3% rate commission which is taken by that man is Riba (interest and/or usury) as it is linked to the amount to be paid back. This is so, because the dealer here is working as an agent and it is a rule that if the agent pays the debts of the one he is representing from his own money and with the consent of his mandator, then this is considered as a loan taken by the mandator. So, if the agent takes an amount that exceeds the amount he has paid and that stays linked with it, then this is a loan with Riba, hence forbidden. But if this agent takes a fixed amount that is not linked with the initial amount he paid, i.e. not a percentage, then this is lawful as this is considered as mandating somebody and paying him/her for that.
2) If this company deals in lawful matters or if that is what prevails in its dealings, but it does some transactions in the way you mentioned, then there is no harm to stay with them, provided you do not deal directly with those forbidden dealings. But, it is better for you to look for another job that is free from what is forbidden. However, if you deal directly in what is forbidden or help in such dealings, then you should quit this job and Allaah will provide you with a better one. Allaah Says (what means): {And whosoever fears Allaah and keeps his duty to Him, He will make a way for him to get out (from every difficulty). And He will provide him from (sources) he never could imagine.} [Quran 65: 2-3]
Allaah Knows best.