To verify that the program in the PLC is identical to the program in CX-Programmer go to Compare (Menu: PLC / Transfer / Compare with ... PLC).
It is possible that even though you have checked the programs are identical one gets an error.

This can happen if in the past the program had downloaded SYSWIN and once the program was saved it converted to SYSWIN CX-Programmer.

The compile method in CX-Programmer runs differently than in SYSWIN.
CX-Programmer has more efficient use of the so-called TR bits. These are internal contacts which are used to help show branches in the ladder diagram. TR bits are programmed in the Statement List programming method.
This means that in that area, the existing program differs from the program running in the PLC.

Click the following option (Menu: Tools / Options)



With this option you can force the CX-Programmer to run as SYSWIN.