They should only hold your check to a few months to make sure things will be fine.
Find out which branch you business deals with and get an account there, then you should have no hold.
I used Scotia Bank, but mainly because I get really good business rates being combined with Canadian Federation of Independent Businesses.
BTW, when I had almost no money in the bank I was treated much differently than I am now.
I would recommend that you calmly chat with them, especially if you have had this job for a while (over 6 months). Or you could apply for an overdraft account.