Indiana Department of Revenue can be very difficult about state income tax withholding amounts which it believes are suspicious or in error.
I have seen cases where the taxpayer has electronically filed but still must mail copies of the W-2's and 1099-R's to the Indiana DOR before a refund amount is released.
Indiana DOR requiring a paper tax return with the W-2's attached is another method that is used to place the burden on the taxpayer to 'prove' that the withholding amounts reported are correct.
You may consider deleting each of the forms that report Indiana withholding tax and re-entering the data by hand. Perhaps there is a character that is not visible to the eye yet causes the software to report this issue.
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