I hate that. It happened to me in emerald. Groudon killed itself probably 4 or 5 times with struggle >.<My SoulSilver save file is going to be three years old in a week, lol.
Anyway, I'm planning to get a 3DS soon-ish, which means I'll be able to transfer Pokemon between games! In preparation for this, I decided to finally capture all of the legendaries in my SS game. I already had Lugia, Suicune, Articuno and Zapdos. So I took my legendary birds, because I love them, but I don't get to use them often, and took off into the Cerulean cave to capture Mewtwo. Took four resets, the idiot kept killing himself with struggle.
Then, I went after Moltres and caught him with little difficulty.
Finally, I took my DS with me when Pirates of the Caribbean was on TV and decided to capture Ho-Oh. Also didn't take too long, but I forgot to save in front of him, so after I had to reset I needed to go through Bell Tower again, lol.
I then proceeded to catch the roaming legendaries. I didn't even realize I already had Entei down to one HP and asleep. At any rate, they were a bit annoying, but not too hard to catch overall.
I'm trying to capture Latios now and hoo boy. This son of a pickle is down to 1 HP, either paralyzed (courtesy of my Ampharos) or asleep (leveled a Haunter for this), I've been trying for like 5 hours and it just won't stay in the damn ball. In addition to that, it takes ages to encounter him again after it flees or I reset. It keeps coming close to where I am, then suddenly appears halfway across the map. Why oh why did I use my Master Ball on Lugia *kicks past me*
I'm not going to give up, Latios, you shall be mine!