Okay, I think I've figured out what makes NTSC > PAL on Invest.
I think NTSC consoles have a smaller cache size than PAL consoles. If an item is in view, or just around the corner, it's in RAM. If it's a bit further away, it's in cache. If it's even further away, then it's not in the game's memory, and the game must load it from the cart in order to display it. So, for the majority of the level, the bot is in cache. If you find a way to fill up the cache with other stuff, the bot is deleted from the game's memory. The game knows the bot's rough location, and will load it when you get near. Understand? Too bad.
Shooting the Falcon 2 creates bullet holes in the walls. The bullet holes and their locations are stored in the cache. Also, in SA, you're never looking in the bot's general direction because it's behind you. So the bot has less chance of being loaded into cache/RAM. Hence why I can get fast bots on SA - I never look at the bot or it's general location.
Now on Agent it's a different story. For the whole level, you're heading towards the bot. So you're facing the bot, and therefore it's loaded into cache/RAM. So the game is keeping track of it, and it goes slower. I've just spent 15 mins playing Invest Agent and never looking at the bot (running backwards

) while firing my F2, I got 3 1:34s. Most likely because I was entering the room at 0:35 when it's usually 0:30. I think the time which you enter the room also affects the bot.
So what makes NTSC > PAL on this level is the fact (Well it's not a fact, but I think it's true) that NTSC has a smaller cache size. It's easier to have the bot deleted from memory. So when the bot is loaded again, the game knows it's general location and loads it in. Sometimes it's a bit wrong.
In case you have no idea what the hell I'm talking about, imagine throwing the bug on Infiltration SA/PA. You throw the bug perfectly and run away. The objective fails. The bug was deleted from RAM, and from cache, so the game didn't notice it was landing. It just went "Hey, they don't have a bug, it's not on the dish, and it's not in mid air so I'll fail this objective." The bug was no where, deleted from the game's memory.
This is also why looking at Jon in Escape makes him run faster.
Nintendo.com has technical info about the N64, but it doesn't mention cache. Then again, it's doesn't mention RAM either, but we all know the jumper pack has 4MB and the expansion pack has 8MB. They are RAM. Maybe the N64 doesn't have cache, and just runs off RAM instead. Makes more sense about the bug throwing thing. If there is cache, it's a very small amount.
So if anyone in the Elite feels like cheating their way to low Invest times, just underclock your expansion pack somehow.