Are you able to determine which Timer0 you are actually getting? Note: If you try to search for the seed based on the IDs you actually get, Pandora's box only searches the min Timer0 set in your profile. If you're getting a different Timer0 consistently, then it may be worth switching.
Your method sounds right. I don't think it matters whether you are starting from a fresh cart or deleting your save file and then advancing your frames. Your seed is already determined by that point.
But if you want to follow the guide to a T, then I guess you could try creating save file first, hitting your seed, deleting your save, and then advancing the frames (without SRing after you hit your seed of course :P).Actually, the guide says to delete your profile before hitting your seed. Reading is hard.
I don't know why that "false" thing happens to be honest. Perhaps when you enter a TID/SID, it searches against the seed and frame you enter to see whether you can get a shiny starter. If you don't enter a seed and frame, it has nothing to search against so it returns "false." That's pure speculation though. I can get it to say true if I enter a seed, frame, TID, and SID. Either way, you're better off checking if the combo works in the main window rather than in Pandora's Box :)