[dvanvoorst]

Actually there was a worse bug in that routine that we discovered last week, and it's likely the actual cause of your problem. The bug was that they were managing their linked list of error values incorrectly - by using push and pop. The result was that the large errors from the beginning of the routine were never pushed out of the list, which caused the average error to always be high.
I checked the source code on GitHub and someone had corrected this issue on 1/7/16, and the updated WPILib that is available now has the correction in it. While the issue that you found might cause a brief issue, I suspect the real issue behind your symptom is this bug which will be fixed if you install the latest library version.