BioConfirm 10.0 Confirmation of synthetic peptides with modifications trouble

We have begun synthesizing novel peptides in-house. For the same peptides made by an outside provider, I am able to use bioconfirm to confirm their identity as well as any partial sequences from degradation. Our synthetic platform results in peptides with an amide at the C-term. I have applied this modification when entering the sequence into the sequence manager as well as using the base sequence and putting the modification in the workflow instead. Neither results in matching. The peak and correct mass are found using the peak finder, but they will not match to the sequence. I have only ever had this problem with peptides with modifications. When manually checking the spectra, the correct m/z are there for both the parent ions and the fragmentation ions, at abundances above the cut-off and within the mass accuracy range for the method. 

What have I overlooked?

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