Hello Enrique,
Ideally issuing 2 / 3 three outputs from a Invoice should not be a problem.
Infact we currently have three output sent everytime Invoice is created - Print-out, email & PDF. All happening simultaneously.
Now in your case, if you are sure that all the config is in please, then please check the Print program & Smartform assignment in NACE & also check from ABAPer whether the Smartform is activated after the last modification.
Further check your Output Condition records in T-Code VV32 & ensure that records for both the Outputs are exactly same.
Thanks,
Jignesh Mehta