The program used to program a SD card just follows rules to copy the image to the SD card. My guess, perhaps a problem between your PC operating system and the copy program.
I have been using Win32DiskImager-0.9.5-binary to image my SD cards. It works well on my old Win7 laptop. Use whatever program that works on your system.
Since the first access point was remembered by the system, it just kept using it. If the system could not connect to the old system, it probably would have used the one in the piaware-configure file.
Glad to hear you found the wpa_supplicant.conf file. Have fun with your system.
That would be the regular place on Raspberry OS (where the Piaware image is created from). I am assuming the file is created on initial install via piaware-config.txt and not changed after you modified that file.
That is normally not working. Linux is not “guessing” what could be right or wrong.