Lunamorte

Huh, did not realize that Method 1 was used commonly in Ruby/Sapphire. That is good to know.

You should not be using the generate feature to begin with; that is more for figuring out what Frame you need to hit for a specific spread/shiny. The ID and SID section are just for determining which PID's would be shiny for that ID and SID combination; they do not actually affect what PID's you can run into. Also, by default, RNG Reporter only shows the first 100000 results by checking only the first 100000 frames unless you changed the max results. Even then, you still have to consider the Seed and Method; if you left the Seed blank it will use a seed of 0 which would probably not be likely for Ruby or Sapphire. If you want to find a pokemon's IV's you have to use the PID to IV tool in 3rd Gen Tools. Using the generate feature isn't practical even to confirm if that PID exists; it is essentially trying to find a needle in a hay stack. As for the nature's, those are tied to the PID itself. For example, if you where to enter Delcatty's PID, D648E142, for a pokemon in pkhex and click off, the pokemon's nature will be set to Relaxed. Also, I just tried to generate Delcatty and believe it uses method 4, as pkhex failed to validate the encounter slot RNG correlation when using the Method 2 spread, but was able to validate it when using the method 4 spread when I set its met level to 8, meaning it was likely caught on route 116 as a level 8 Skitty. I found its starting level by using the Sapphire Encounter Table. I am assuming they are from Sapphire based on Kyogre. I've generated all six of them myself using this information. If they had multiple valid spreads, I simply picked the top valid one and preferred Method 2 over 4 if both were valid. EVs are not fully saved when you mix records (the game just evenly distributes the EV's to all of the stats for secret base pokemon) so I left them at 0; you can set them to whatever you want in pkhex. PP Ups are not saved either. This is probably as close as we can get to the originals with just the secret base data as it sadly does not include the IVs. I tried using an Action Replay Code to catch one of the pokemon from the secret base and their IVs were all set to 15 when I looked at them with pkhex. 0301 - DELCATTY - 0CCAD648E142.pk3 0330 - FLYGON - A945DBA87B9A.pk3 0334 - ALTARIA - 1E343EAB3A50.pk3 0382 - KYOGRE - 83F527B38389.pk3 0384 - RAYQUAZA - C9304B24668C.pk3 0260 - SWAMPERT - 6FB93BE184BF.pk3

They appear to be correct from my testing, when I compared them to the PID's of my own pokemon based on what pkhex tells me; I am getting IV's for them on RNG reporter. Are you using the Gen 3 PID to IV tool on RNG reporter? Because I was able to find IV spreads for all of them on RNG reporter. I attached images of what I got from the PID to IV tool from RNG reporter. Kyogre, Rayquaza, and Swampert (assuming it was your starter) should be using method 1. The remaining three are probably method 2 (technically H-2) if you caught them in the wild; if they were hatched from eggs, there basically stops being a correlation between IV and PID. I am not fully sure what the different seeds mean however.

Changing anything on the dumped save won't do anything since the issue is with the save on the cartridge. There is a possibility of something physically wrong with the cartridge itself, because if replacing the save via TWLSaveTool does not work, something is very strange. Just to make sure, the emulator you were using, was it Dsemume? Because I believe Dsemume saves its saves files as .dsv, which would not work on a ds cartridge. I think there is an option to export the save file as a .sav file, by going to File and Export Backup Memory on Dsemume.

I recently found a Secret Base Editor for Emerald on github, forked it, and have been adding onto it for my own use/fun. I was able to get the following information from your save file: The ID/SID combo matches with what you posted earlier. Secret Base mons don't have any other info past this. You would need to use the PID to figure out its IV's, and it does not keep track of any ribbons or condition. If you can get me the save file, I can try to extract the PID for them from it. From there, you can use the PID with rng reporter and pkhex to recreate them.