Okay, that is a good visual explanation and helps a lot with us trying to understand what you are seeing. I am still pretty darn sure I don't have that issue on my 3G running 3.0, or if I do, it is rare enough that I don't pay it much mind, but I will try to reproduce and pay attention to this specific animation and report back here (I switched to my 3GS over the weekend, so 3G is not on me at the moment).
BTW, since Bat Commander (actually was wondering if that was you, TheSpaz, based on some of the things said in the pre-edited version of the post) asked earlier about my setup, I'll bite, and make it as detailed as possible (I don't know that this will actually help anyone, but I don't suppose it can hurt either):
I have 3.0 build 7A341 running on an iPhone 3G 8GB. It is jailbroken, but I try to keep a sharp eye on my use of JB software and what they are all doing at any given time (no extraneous daemons running in the background that I don't know about, etc.), and have eliminated certain things from my list of JB software based on past bad experiences. This means NO WINTERBOARD; in my experience, enabling Winterboard themes is a good way to slow down the phone and cause some of the animation stutters that it sounded like TheSpaz was talking about before (although I realize that he doesn't use Winterboard himself), ESPECIALLY if you theme the keyboard (keyboard gets HELLA laggy if it has a Winterboard theme applied to it, or at least it did in 2.x; haven't bothered to try in 3.0 yet).
I have Backgrounder for 3.0 and SBSettings installed. SSH is always enabled. Although I use Backgrounder extensively, I always quit out apps when I am not actively using them. This INCLUDES Apple's own apps which multitask natively; I religiously close out Safari or Mail, for example, when I am not using them, by using the Processes toggle for SBSettings. This is to keep as much available RAM free as possible as well as to reduce possible CPU usage (I don't trust Apple's software any more than I would trust anybody else's in the background; in fact, that Apple surreptitiously allows for their own apps to run in the background but won't allow third-party apps to do so gives me all the more reason to not trust them.)
By extension, I don't like it when apps launch themselves and start doing crap without my knowledge, so e-mail push/fetch is completely turned off; I check e-mail when I have time and don't need to know the exact second that a new e-mail arrives. Once I'm done, I force-quit Mail.app.
I also only enable other features in the OS when I need to use them, so Location services are off unless I am going to run a location-aware app, and Bluetooth is off unless I'm going to pair something to the phone, etc. Of course, most people do this anyway in an effort to conserve battery life.
Other than that, don't know what to tell you. Perhaps my diligent policing over the actively-running software on my phone contributes in some way to my better performance (or perception thereof). For me, though, it's all just force of habit, so it's not like I am actively thinking about it all the time. It just happens.
-- Nathan