So, after some reading I think I have narrowed it down to 2 problems that I had introduced. First one, I think I had the bed too close to the nozzle, this was not allowing enough material to come out properly. Secondly, I had over-tightened the 4 silver thumbscrews on the top of the nozzle assembly.
Combination of those 2, once I corrected those I have been getting great prints again. Hope this may help someone diagnose in the future
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Anders Olsson 136
Are you by any chance printing at flow rates below 100%?
There seems to be a strange bug in Marlin that does similar things to my prints if I go below 100%: http://umforum.ultimaker.com/index.php?/topic/7764-underextrusion-when-flow-is-set-below-100/
If this is not the case I guess something is wrong with your teflon insulator (deformed/too small inner diameter).
Or your filament is too large or damaged from grinding.
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