A bit of an update: As an experiment I dumped my SoulSilver cartridge to try using that ROM with my save file instead of the ROM I had used before, but it still wouldn't load the save file. I AP patched the ROM both times with DS-Scene Rom Tool. Anyone have any thoughts?
My next experiment was to try the ROM without AP patching it, but that didn't work either. Next idea is to try re-dumping the save file from the cart.
Oh man I just realized that I provided the wrong info about my backed up save file in my first post. The size is 128KB and not 1024KB. Sorry about that.
**Success! I tried re-dumping the save file with Checkpoint and this time the file came out as 512KB, and has loaded successfully. Don't know what happened the first time, but all appears to be in order now.**