Ok so I've managed to fix it.... If you have games on another HDD/USB than system, F1 will eventually die. I have tried on desktop and laptop to see. Basically fresh install of Batocera on HDD does everything correctly, however if you already have files saved on HDD with roms many things get messed up. The folder structure does not get updated and many config files will start from the disk you keep the roms. For example: My laptop still had Batocera 5.22 where there were two folders MSX1 and MSX2 but the new folder is just MSX. System did not see any games in these two files and I had to copy them over. OR cursor has completely vanished in F1 menu when updating and the applications simply froze the display when opened.
I have taken the HDD out copied files from the fresh install 'share/system' folder to my ROMs HDD 'share/system' folder and everything got fixed ;-) The game folders I had to move myself, which is fine for smaller files. 5.24 has a fancy 'Favorites' and 'All Games' folders that was either not shown in previous versions or was not there. I do like to have them but could not see then before the move of files. ;-)
I assume fair amount of issues I had with Batocera was due to that. I used the same HDD for ROMs since 5.21 on my laptop and maybe 5.22 on my desktop.
Is there a way to get the 'ROM-s' HDD/SSD/USB to update or get something like first time run popup explaining the 'structure' change ?