Verify the MD5 hash of your game dump first (use a website like redump.org or GameTDB.com). If your MD5 hash doesn't match their, redump your game until it does.
Try turning off cheats as well. This last suggestion is a shot in the dark, but games that use the Zelda ucode on the DSP (this is one of them) sometimes freeze with HLE audio, probably because Dolphin's HLE implementation is correctly signaling when a sound ends (which apparently is used to signal the start of new scenes and such). I know Pikmin and Wind Waker suffer from this, but I've never heard of any one playing TP and getting this problem, but still, trying LLE audio might be worth your time. Other than that, your settings look fine to me.
Try turning off cheats as well. This last suggestion is a shot in the dark, but games that use the Zelda ucode on the DSP (this is one of them) sometimes freeze with HLE audio, probably because Dolphin's HLE implementation is correctly signaling when a sound ends (which apparently is used to signal the start of new scenes and such). I know Pikmin and Wind Waker suffer from this, but I've never heard of any one playing TP and getting this problem, but still, trying LLE audio might be worth your time. Other than that, your settings look fine to me.