Syswin and CX-Programmer have separate compilers and they treat Temporary Relays (TRs) in a slightly different way. This results in different compiled code for any program that contains TR's. All versions before 2.1 compiled an imported program as part of the conversion process. Therefore the imported CX-Programmer code was different to the code in the PLC, if it was downloaded by Syswin and contained TRs.

A successful program comparison operation between CX-Programmer and the PLC was therefore impossible.
To counter this problem CX-Programmer V2.1 was altered so that it no longer compiled automatically during a conversion process. This allows a successful comparison operation to be performed. The program can then be compiled either manually or by saving. The compiled code will then no longer compare successfully, so the program should be downloaded to the PLC.

Merging comments and symbols from a stored file (Transfer "From File") will also force a compile on a converted program so a compare operation should be performed before merging.