Put a debug breakpoint in your code, and then run RSA3 again in Update Mode delta (D).
Check if the debugger goes into your breakpoint - it should.
If it doesn't , it may be your user exit is not activated correctly, or there is some clause in your code (check for IF-ELSEIFs) that bypasses the customer exit only during delta loads.
I hope you did the user exit correctly, because these things normally do not happen at all when implemented correctly. There are a 101 different things that could've gone wrong when these things happen. My advice is to check and re-check your user exit code in the program ZXRSAU01 to make sure everything is setup correctly.