We use the OAA A320 simulator near LHR. The MCDUs are real, but although you would never know it, the FMGCs are actually a PC based emulation. The emulation is good, but as both the software and hardware are different from that used on a real A320. This set up should be treated with caution. If it works in the sim it may not work the same on the aircraft and vice versa.
To get around the OPs problem. If you cant copy the active flt plan (X to Y)into the secondary. Delete and then INIT the secondary instead with flt plan from X to X and complete the SEC PERF APPR page.