3 possibilities:
1) You amended so the transcript has the amended amount but then AGI database uses the original amount.
2) You filed late after the due date so the database has a zero AGI amount - try using zero for your AGI.
3) Since the e-file AGI database is separate from other IRS databases, it might be en error and there is no way to fix it so the only option is to paper file.
**Disclaimer: This post is for discussion purposes only and is NOT tax advice. The author takes no responsibility for the accuracy of any information in this post.**