I retried Pokemon Soul Silver on my M3 DS Real with 4.8X software (the most recent), and within 5 minutes of in and out and in and out and..., it froze. I'm not 100% sure though, because Windows Vista is being mean to me, and isn't letting me delete the last part of the old system file (which I just renamed for the new file to exist). If I can get it off, I will check again. But, AP still exists with unpatched (if there even is a patch!) Soul Silver. :'(
Format your MicroSD, and reinstall your firmware. If you had to rename something and still have the old files on there it may be causing issues. Remember to backup your files before formatting your card.
I just started reformatting device defaults, so, I'll see... *Falls to knees and begs God that this works* Post Merge: [time]1269829456[/time] OK. Reformatted defaults, and I tested both 4.7h and 4.8x. Both crashed. :'(