Go to the game's properties in your steam library and make sure you have steam cloud enabled for it and also go into steam's settings and make sure you have cloud enabled there. If that doesn't help, try alt tabbing after you level up and back up the file located in C:\Program Files (x86)\Steam\userdata\numbers\22350\remote. If you save it before you shut the game down, it should be the most recent version, so maybe you can use the back up (the good file) to replace the file that keeps getting reset *shrug*.
Thanks very much for the help, I managed to figure out what the problem was with your advice. A couple days ago my anti-virus software updated, and my computer went into safe mode for whatever reason. Anyway, the majority of my computer files were automatically set to "hidden" in order to protect my computer. Apparently the game cannot overwrite old save files if that folder you mentioned is set as "hidden". As soon as I switched it back to normal, the problem cleared up. Thanks!