I encounter this problem 5 months ago.Day1 i say OK.Day 2 i try a different browser , clear cache , history etc . Still didn't get the 50 extra stamina .

What i do in order to get the bonus stamina is : Stay in hotsprings while in browser for 1:57:00 (or 1:58:00 if you are a Jonin Medal user) then exit . Resume Hotsprings proccess from the mini client and you get the bonus 50 stamina . I know this can be frustrating but this is the way i get the bonus