can you post the exact code you use for converting degrees to radians. Are you using fixed or floating point arithmetic?
Where do your sin and cos functions come from? Are they in a library included with the mill controller software? Do you have a way of examining the values for x and y other than where the milling head starts? Do you have debugging facilities for your program?
short story is that your formulas are correct but the devil is always in the details.
Is your error consistent? Will you always get the same error with 90 deg. for example?