Is what my boss doing illegal with my paycheck?

I work at vector marketing. (DO some research on it...it is not illegal but it is deceptive as all get out so i am already wary) well i use to work at one office and I was always given a personal check that said "Titan force incorperated" on the top so i felt a little better about cashing it because even thought it was a hand written check from bank of america, it had a company name on the top. I got pay stubs that were on a hand written form and i was able to file my taxes no problem. well i moved offices closer to home and not this manager has only given me 3 out of 4 pay stubs and even though the stubs show that taxes were taken out, his checks arent from the company, they are from his own personal bank account. My question is, can someone do this (he is an independent contractor but works for the company vector marketing, he is the "district manager). My sister says that what he is doing is illegal and i should report him to the irs because for all i know he could jsut be syaing that he is taking taxes out and isnt.