Hmm. So let me make certain I understand what issue you're experiencing and how you get there:
1. You load the Zelda OoT ROM in PJ64.
2. The N64 logo spins, the opening cut scene begins and you press Start (or A) once or twice to arrive at the game file menu.
3. You select your file ("Jake") and select "Yes".
4. The next thing you see, you are stuck in the standing position on the ladder in Zora's Domain.
Is that correct?
When I run the ROM with the save data you posted, I'm unable to reproduce this issue. I am presented with a single file ("Jake") with all the stones and medallions and when I select it, it starts me off in Link's house as a child (which is normal, assuming the game was saved when Link was a child and not in a dungeon). So my suspicions would be that either (1) the ROM is bad, (2) a save state is inadvertently being used, or (3) cheats are inadvertently being used. Since you stated you are not using save states or cheats, I would try a different rip of the ROM and see if that makes a difference.