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

Well darkness000, I was addressing his second issue he had with only being in the 100s since its perfectly normal

The first is certainly an issue no idea how its even possible to have less than the max either 350 or 500 for being logged off for 2 days.