Anyone else have this issue? I have two state returns that are almost evenly split in my income. The one state was perfectly fine but the other doesn't want to take my state AGI from my W2. When filed, it changed that state's AGI to equal my federal AGI. Customer service helped me to go in and edit it but it already had the correct state AGI so I just resubmitted it and sure enough, when I downloaded my return it showed the federal AGI again. Customer service said there's nothing that can be done at this point and we just have to wait until it's either accepted or rejected and then they'll assist in getting it fixed. Sounds like we're just delaying having to deal with it. I think there's a bug in the system and I doubt that will get fixed based on how they treated the issue.
First, your AGI consists of more than just a number on a single Form W-2. AGI includes all sorts of income, and you may also have adjustments that offset some of your income.
Second, it's not at all uncommon for the AGI on a state return to differ from your federal AGI. Different states have varying policies of what's included in their AGI.
Perhaps if you share what your seeing on your federal and state returns, we can help. What state returns are you filing?