Before entering 1098T/AOTC data we have a $1000 refund. Once I enter 1098T/AOTC info it shows $3300 refund. I thought AOTC was limited to $1000 refundable if not tax due?

You are correct in saying that the maximum refundable part of the AOTC is $1,000.

In your case, you may also have some non-refundable AOTC. You cannot have non-refundable AOTC only when your tax liability is zero. Having a refund before entering the AOTC does not necessarily mean that your tax liability is zero. The refund means that you had tax withheld (and other tax credits) of more than your tax liability. So if you had some tax liability then you would benefit from the non-refundable part of the AOTC also.