Same problem here - Illinois full-year resident, but my husband's W2 shows income in 7 different states, including NY.
His W-2 shows his full income (let's just say $100k to make it easy) allocated to IL and also to NY (this is a known NY thing - they want your full income reported to their state to make sure your tax rate is as high as possible, and then they prorate it based on how many days you actually worked in NY - I guess they must have a graduated state tax rate while other states do not?), and then the other 5 states show a small amount each.
So when you add up all the state line items in box 15 of his W-2, the 7 states add up to, say, $210k ($100k IL, $100k NY, and $10k among the other states). ACTUAL NY income (as figured out on our NY state nonresident tax return) is more like $2k. But the amounts on schedule CR only show the real amounts to each state (the $2k to NY) so it would add up to $100k, his actual income.
The only way I can see to force the W-2 numbers to match the CR numbers is for me to not accurately type in the W-2 numbers. I'm uncomfortable with that. I don't mind filing the state tax return on paper; I just don't want it rejected or whatever.
