Hi Alex,
all available resolutions in KODI, including those you want to select for the whitelist, are based on the EDID information. If the EDID information is incomplete/incorrect, then the GUI settings may change with each restart. Details confirming this are only visible if you provide a link to a debug log. -> https://wiki.libreelec.tv/support/log-files
If the HDMI handshake fails after a successful start with the same resolution, it indicates more for hardware issue like cheap/bad HDMI cabeling or firmware issues of devices. One of known trouble maker could be the Argon ONE case as well. If you use such case, please try again without that.