Super late bump with more info!
Okay, so I must apologize. Today, I received the cart version of Seiken Densetsu 3. Of course, the first thing I thought to do was to test this "bug". To my surprise, it actually happens on the cart! This is NOT a SNES9x-specific issue!
Determined to get to the bottom of this madness, I went through all of my various computers and tracked down every save file and emulator I had for this game, and sure enough, in each one the sequence of items you get from item seeds is always the same, no matter what you do, or how many times you reset. However, the sequence I was repeatedly receiving was DIFFERENT for every save file.
Returning to my cart copy for the moment, I decided to try getting a little farther in the game before saving and trying the seeds again. Simply progressing and then saving does not help, but to my great surprise, when I reset the game and tried the seeds again, the sequence was finally different!
So we finally have the answer - The sequences of items are generated when you start the game, and the seed for the randomizer is the content of your save file. It seems like the stat that actually matters is EXP, simply staying at the inn again and saving did not change the sequence. I suppose this makes sense, since the SNES has no internal clock, but the fact that they generate the sequences when you boot the game really threw me off.
Oh, and this also explains why I thought ZSNES wasn't doing it. I was playing the game at the time and did the following sequence of steps:
- Check sequence
- Check sequence
Which generates a different set of items since my save file changed. However, had I continued to reset, I would have seen the same ones over and over again. It was simply luck that I got what I wanted on the first reset and never tried it again.
Long story short, you can mark this bug as "solved" or, rather, "non-existent". It was just some really convuluted logic in the game.