They call it stamina, but a better name would be immediate health; while health should be called overall health. First, your stamina goes down, not through use, but injury. When it reaches zero, you start affecting your health. To regain complete health, you first improve your health, until it's up to its maximum potential. Then, you start healing your stamina, from zero up to its maximum potential.
If resting doesn't restore you at all, chances are you're suffering from some negative condition. Poisoning and disease will affect you in this way, and there should be some notification of this on the stats screen for each character in your party. Note, you can't heal up to maximum out in the wilderness, though you can get close. For that little extra bit, you need to use an inn, or healing potions.
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