Hired as a Independent contractor by former employer.

I lost my job in September 2020 when the company closed the office in our city.  The same company hired me to do work remotely for another office, as an independent contractor in March of 2021. During this time I did not receive benefits, and was paid on a monthly retainer  which amounted to a fraction of my former salary. In July the hired me as a full time remote employee. The job I am doing now has some similarities to the job I lost in 2020, but it is not the same. For instance, the old job was a managmenent position, and this one is not. The salary is also quite a bit  lower. As I'm going through the deductions for the four months I was self-employted, it appears that I am being penalized for working freelance for a former (and future) employer. This doesn't make sense, because I definitely wasn't an employee during the time I was working as a contractor. I'm a bit cofnused. Any ideas?