Hey, I had the same problem, but Pearl crashed when trying to look at Cresselia. The way I fixed it was by loading the modified save file into PKHex, and I removed Cresselia's seen and caught check marks. I then exported the save file, loaded the new save into PKHex and re-checked Cresselia. I exported it a second time and when loading it on my 3DS, it doesn't crash anymore. Hope this helps.