I am single. I lived in NY State from Jan 2007 to April of 2007. I moved to the State of Arkansas in April of 2007 at which time I became a permanent resident. I filed my 2008 Federal and State returns and neglected to include my NY state income. The following week I had a friend in NY prepare an amended Federal, NY State and Arkansas return. Well... when she calculated my income percentage for the State of NY she came up with 28.65% - NY State Amount 9,868.00 / 34,439 Federal Amount. These are the amounts on my W-2's. I ended up owing the state $382.00.

Since then the State of NY sent me a letter saying I owe an extra $1,032,00 because my income percentage should have been 100%. Are they correct? I protested their claim... the only way I calculate 100% is if the NYS and Federal column are identical and they are not. How can they tax me 100% when I only made 28% of my income in that year in NY State.

Did you file NY return as a part year resident or a full year resident?
Only income earned while in NY is taxable in NY.
For Arkansas also you are part year resident and your Arkansas income is income earned while in Arkansas.

Send NY state a copy of your Arkansas return. That should convince them about the percentage of income that is NY-sourced.