I think I found the problem. I bought a brand new 4th generation Ipod touch, I didn't need the newer 5th generation. But I just found out that the 4t generation Ipod touch don't have a biult-in GPS chip, it rely only on Wi-Fi signal. In metro area you don't see the difference but on my rural commute Wi-Fi signals are rare so that's probably why I ''jumped'' from one side of the river to the other.

Nothing to blame on the Runkeeper app.