Asus's GPS troubles with the Transformer Prime don't seem to have been easily resolved by the recent firmware update, and Anandtech claims to have the answer. A teardown of the Prime didn't reveal much untoward, but does show that the spotty GPS reception is down to the tablet's fundamental hardware design. Unlike the original, plastic Transformer, the Prime has a fully aluminum body which doesn't play too nicely with wireless signals, and unlike the iPad there's no RF window or speaker grill to mitigate it (it's worth noting, though, that the Wi-Fi-only iPad with which the Prime directly competes doesn't have a GPS unit at all). For its part, Asus has admitted that the tablet's design does hinder wireless performance, and has removed GPS functionality from the list of specs on its website.
Asus Transformer Prime teardown reveals cause of GPS issue
Anandtech has posted a teardown of the Asus Transformer Prime, and given insight into what is causing the GPS issue. The aluminum build of the tablet appears to be at the root of its connectivity issues.