Mitsubishi unable to apply changes in program

Hi folks, one of my project was installing new analog module Q66AD-DG to Mitsubishi redundant PLC Q12PRH. All the configuration that had been done in GX developer and program in PX developer were working. I had compiled and downloaded the program. However, when I power off the PLC and power on again, the applied changes was not inside the PLC, the PLC still used the original program.

We had to reformat the PLC. After that, write an empty program to Mistubishi PLC, and then redownload the correct program into the PLC.

Is there any experts mind to share what is going on here?

I can think of a couple of possibilities, the PLC parameters under PLC File was set to load from Memory card rather than standard ram or under boot file the program(s) were being loaded from memory card.
I have never used these as I have always used standard ram I believe that when doing an on-line change it will only change what is in the standard ram, on power up if the parameters are set it will load the program stored either in the ram memory card or rom. so overwrite the program in standard ram.

Thanks for your reply. From your explanation, that is the only possible reason can relate to this problem.

I configure the parameter in GX developer and modified program in PX developer. Based on past experience, I just press Online -> Download in PX developer.

To solve this problem, after I had performed the download in PX developer, should I open up GX developer project again from PX developer and select Online -> write the program memory to ROM? (based on GX developer version 8 operating manual)

I saw there is another option, write to PLC (Flash Rom). I'm a bit confused here. Any experts can clear my doubt?

I have never used PX developer so cannot comment on it's use, again I never use the rom on PLC's I have always used standard ram, the only reason I would use rom or SD (flash cards) is when the project is complete and no more changes are likely, generally I only use the standard ram & ensure any batteries if used are replaced every year regardless, Having not used rom or flash cards I have no idea if you can make modifications on-line & the program will probably only be copied over to the standard ram on boot so changes done on rom would not take place until a re-boot. this is what I think is the case but not having any cards available I am not sure exactly what happens.