Hi,
there shouldn't be such big differences between running SWAT+ with SWAT+Editor and R-SWAT.
Be SURE that you used the same executable SWAT+ version and debug or release mode.
You could test it manually by doing the following:
Check the calibration.cal from the TxtInOut folder of R-SWAT and SWAT+Editor if they are the same
copy the same SWAT+ executable to the TxtInOut folder of
R-SWAT and SWAT+ and run it manually => then check the output if they are identical
Just let me know if you get the same simulated result this time