This happens when the credit card type name in the System Defined Fields in the database doesn't match the name that is on the donation form.
For instance, if the Name field for MasterCard (seen correctly below) was spelled out "Master Card" with the space, and the eCommerce has it correctly as "MasterCard" the system will still process the gift but will say "None Selected" on the gift record (Image Below).
To fix this user will need to do the following steps:
1) Select Management
2) Select System Defined Fields
3) Select Credit/Debit Card
4) This will automatically put you on step 3 "Values" - Select the credit card type (blue link) you need to fix
5) Change the value in the Name field
6) Click Update
7) Click Save and Finish
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