I ran a 5K with both iSmoothRun and Nike+ running apps on an iPhone 5 (simultaneous, not one then the other). The Nike+ decided that I had reached 5k about 0.3k before the iSmoothRun decided I had reached 5k.
Alan (Still doing a 5k about every five days).
The GPSes in phones aren't generally that sensitive, either, and it doesn't help that the phone's often in a pocket. Plus if you run through a forest, tall buildings, etc. it can have quite a significant effect on the results.
This is one of the reasons I've always been against putting GPS into Get Running itself: I think a beginner has enough to cope with without making the app possibly less reliable and more confusing.
A lot of that is based on my own experiences running with other apps that did have GPS built in, where sometimes it would work, sometimes it wouldn't, sometimes the results would differ wildly from reality, and sometimes it would even seem to crash the app. It also drains the battery on your phone quite fast -- my phone only just made it to the end of my first half marathon with the GPS running.
In the end I bought a Garmin Forerunner GPS watch, which has a great GPS unit, goes on your wrist where it can always "see" the sky, and has a rechargeable battery that lasts for a lot longer without leaving you with a dead phone if it dies, too. They can throw your results up automatically to Garmin's own site -- some other sites support import of Garmin stuff (RunKeeper supports my old watch, not sure about the newer ones: if you're in the market for a GPS watch, check that it'll work with your favourite log-keeping site before you buy, if that's important to you!)
So, if you want really good GPS results, I'd recommend a dedicated runner's GPS like the Garmin. On the other hand, you've got to spend more money, have an extra gadget around the place, and remember to charge another thing before you go you out...