You always get the first refund. In fact you should not even do the amended return until the first return fully processes and you get the refund. The Amended return should only be for the difference you get back or owe. Did the 1040X have a tax due? Ignore the payment voucher that prints out with the 1040X. If you have a tax due just include a check when you mail the 1040X. The voucher is for what your original 1040 return would have been if you had done it right including these changes.
You can confirm this by printing your amendment and looking at the 1040X. Line 18 should be your original refund amount and line 21 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.
