You probably need a combination of both! If my understanding of the problem is correct, then manually creating a sales order for a credit blocked customer is behaving differently from ones created through EDI. This may be a configuration issue, it may be a "feature" of standard SAP, or it may be that the custom condition has an error in it. The first step would be for a functional expert to check, then bring in an ABAPer if nothing is found.
It is entirely possible for a process in SAP to run differently according to whether it is done manually in foreground, or, for example through EDI subsystem, automatically in background.
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