Unfortunately, I can only advise that you better rely on your manual saves, as the game itself seems to be buggy in this case. My auto-saves normally work, but just today I have also figured out that the game did not auto-save at all during my newest playthrough, although it was always telling me that it actually does. Funny, there is not even an option in the menu to shut down auto-saving at all. Yesterday I even had to scratch my second playthrough and start from the beginning again, as the game always threw me back to the main menu during the loading process, after I have finished the western map holodeck mission, the one that you can choose to do before going to the scavenger base. So, again, don't trust the game when it comes to save your actual game, and better rely on your own saves.
PS: I have not tried this yet, but maybe this solution could work:
https://www.gog.com/forum/star_trek_voyager_elite_force/game_exits_to_main_menu_upon_saving_and_later_randomly "Open the econfig.cfg file or launch the game and open the console.
Find com_hunkmegs value in config file and increase its value or type /seta com_hunkmegs x in the console, where x is a larger value than the default one. Default is usually 36Mb, setting to 72Mb seems to also solve the issue with the game resetting back to the main menu when a new area is loaded."
