Hmm.... Your situation sounds a bit strange

However basics of stamina gain is 10 per hour or that's 1 per 6 minutes. In hotspring its 1 per 3 mins or with Jonin medal activated its 1 per 2 mins, additionally you should get 50 additional stamina for completing the 2 hours. At 0500 and 1300 you should get a boost of 100.

So what you should be seeing at the end of a 2 hour wait in hotspring is 110 or 130 with Jonin medal.

Hope this helps