Make  sure the original refund or tax paid and the first amended amounts you paid or received shows up on the 2nd amended return.  You may have to override the amounts using Forms Mode.

You can confirm this by printing your amendment and looking at the 1040X. Line 18 should be your original refund amount and line 22 should be your additional refund.  If you paid on your original return it will be on line 16.  If there is an amount owed with the amendment, it will be on line 20.

You have to include a check for a tax due when you mail the amended return.  Do not use any vouchers that may print out.  The voucher is what your original return would have been if you didn't need to amend it.

If you have a refund they will mail you a check.  They don’t do Direct Deposit for refunds.