Is working as an accountant in a company that started with capital from a loan, on which a "loan commission" is paid instead of interest, permissible or impermissible?

Your work at the company is permissible because its operations are in permissible areas. It does not matter that its capital came from an interest-based loan. What is called a "loan commission" is usury (riba), and what matters are the realities, not the names. Any stipulated increase in a loan contract is usury by consensus. The important thing is that your work at the company be in a permissible field not related to interest-based loans.