Add to that the Shiny Entei can't really be checked according to the PokéCheck FAQ. I'll have to inquire on ARed Events as I know ARed Pokémon was listed in the "illegal" group, but now I'm questioning every single one I've received. Even so, they all SEEM legitimate at first glance; my only doubt is the "received" date in each case.
Again, I can confirm the Shiny Nincada, once imported, IS legit. I even have Lv.1 Dialga, Palkia, and Giratina in SS;, I did use AR to repeat the Arceus Sinjoh Ruins bit three times, but each "baby" is a legitimate one from the sequence itself and not hacked otherwise (besides, you can later repeat it without Cynthia to get a second, though I am unsure on a third). I have a Lv.1 Regigigas - also legit. I do have a lot of legit. ones, but as I said, there's no way to know if any are legit. or not.
AS FAR AS I KNOW, the Shiny Entei and LArvitar are legit.; I admit I've screwed up my own game with a wrong date by catching a swarm Pokémon "before" defeating the E4, but it's due to changing the date after beating the E4 in an attempt to try something. Larvitar is probably legitimate. But the possibility does exist that someone created a code the day it was announced. Larvitar CAN be PokéChecked in Battle Videos apparently since it's not banned from battle facilities, however, I haven't used one as such and have no idea if it would be flagged.
Keep in mind that unless you captured Shaymin and Deoxys yourself (I presume you did), I likewise can't confirm EXACTLY where they came from. It's the risk I take. That's how I ended up with a Lv.3 Jirachi I eventually said goodbye to, and a Lv.37 Arceus. At least I cleared the entries for them! And later, I did get legitimate ones. :)