Test cube problem

I've had my SD3 for a few weeks now and all I can say is that I have learned a lot and haven't slept much.  Even though I was printing out of the box OK but I was having problems with prints as they got larger so I finally went back and started calibrating my printer like I should have in the first place.  Things are working much better now, and even my larger prints are sticking like glue to the platform (glass and hairspray).  My problem right now is in my test cube and cylinder.  When it goes to start a new layer it's not extruding enough plastic.  The picture below is by far the worst of the ones I have as they were printed together.  When I print them alone they look better as there aren't any drips moving from part to part.  I'm guessing that this can be corrected later with good retraction.  My main concern now is getting the cube to print properly.  My settings are below and the thickness of the 2-4th sides of the cube measure right around .42 mm in thickness while the first side comes in closer to .34 and has the visual gaps you can see right through.  It seems like upon moving to the next layer it's retracting filament and not getting enough to start that layer.  I just don't understand as I'm not telling it to retract upon moving up a layer.  I copied my settings from my EEPROM below and told them to SAVE but is there anything else i have to do to have these settings take effect?  I pressed a reset button on the back of the SD but I'm not sure if that was needed.