I mostly do Windows, so I am not the best resource for Unix behavioral issues.
If I understand you correctly, you have an application that is setting RC=0010, but the UC4/Unix agent sees the failure as RC=0001. I would be trying to figure out why. There are many possibilities.
Maybe the application is setting it back to RC=0001 before it finishes execution?
Maybe you have another process script instruction executing after the application that sets it back to RC=0001?
Maybe you have the OutputScan feature turned on and it is setting RC=0001?
Maybe this is a normal behavior of the UC4/Unix agent?
I hope someone with more Unix experience could chime in here?