There are some differences in the way Syswin and CX-Programmer compile program code. In particular CX-Programmer is more efficient when compiling code containing TR's (Temporary Relays). Unfortunately this results in a "Compare Unsuccessful" result when CX-Programmer compares its compiled code to the PLC code downloaded using Syswin.
From V2.1 onwards, CX-Programmer no longer automatically compiles after file conversion. This enables a successful program comparison to be made.

After the comparison , the code should be compiled, and if possible downloaded to the PLC. Otherwise once saved or compiled it will no longer record a successful comparison.