My printer was plagued with this problem until recently. If you read through this thread: http://3dprintboard.com/showthread.p...agon-vs-E3D-V6

It shows how I fixed it, I tried about 13 different things before getting it fixed. But at the end it was the fact that I am using 1.75mm filament and the extruder is optimized for 3.0mm. This means the tube that feeds the filament from the hobbled bolt to the extruder was way to wide. So after printing for a while it would flex inside of that tube and would not having a good feed and start to eat the filament. I solved this with a small piece of aluminum that reduced the diameter of that tube to 2.0mm's.