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Looks like you need to relevel your build platform.  The first picture looks like the extruder nozzle is too close to the platform and as a result the nozzle cannot extrude plastic.  That's consistent with the extruder making ticking sounds and the blank holes.

Also, you will likely be better served using the makerbot-operators group or the jetty-firmware group to assist in diagnosing this.  Comments here really are not a viable vehicle for doing support, especially given that Thingiverse has been down off and on recently, and for the past month or so has reportedly not been good about sending Thing authors notices about updates to comments.  (I.e., Jetty may not be aware that new comments are being posted without having to proactively look for new comments.)