I've had similar issues before and after the update. Google Navigation has no problem, especially when I am in the car, but on the regular maps, it tends to show me a mile or so away from where I am (usually inside)
To remedy this, I disabled "use wireless networks" under location and security settings. Works pretty well. Your best bet is to disable wireless networks outside, and use them inside.
On a similar topic, I can't seem to figure out how Latitude updates on the maps... It will show me a mile away from where I am, and show girlfriend on the other side of town, even though she is sitting next to me with maps open. Any suggestions?
Also, please remember that alot of these features and/or technologies are still in beta. GPS by wireless network is pretty new, and it needs a lot of work before it is where verizon, google, and motorola want it to be.