State tax filing

Follow-up question on this...

 

I've been in Michigan, working for a NY company at my convenience for several years and every year I have issues with my NY return. TurboTax asks you to quantify how many days you worked in NY vs. MI, which I do (hotel receipts make this very easy). It's normally 10% NY and 90% MI, so TurboTax projects a large return from NY. However, EVERY year, NY audits me and adjusts the return to be lower and I can't figure out why. 

 

It's frustrating because if I knew in advance exactly how much NY would adjust my return for, I would just submit the original as if I spent that many days in the state (because the result is me getting taxed in MI as if I worked there 90% of the year AND taxes in NY as if I were there, say, 40% of the time instead of the 10% I submitted).