Unanswered Having trouble with first layers

On every shape that I attempt to print, I'm having a lot of trouble getting the beginning layers to print correctly. The resulting print, which should be symmetrical on both top and bottom, ends up with one side too short.

I've been using this as a test print with mixed results. http://www.thingiverse.com/thing:941177

So for that shape specifically, I'll end up with one side of legs that are 20-40% shorter than the legs that print at the top of the shape (at the end of the printing process)

I've watched closely as the printer begins its process on this shape and others, and it almost looks like the starting layers don't extrude enough filament -- just very, very thin layers, so thin that they almost seem transparent.

I'm so far just using Matter Control 1.5 and tweaking settings from the presets Low, Med, High.

Unrelated question: are these wires supposed to be disconnected?
http://imgur.com/a/H2c6r

 

Here are some photos http://imgur.com/a/nla4c

I'm using a refurbished R1+ - this is only my second day printing with it so I'm starting from the beginning.

I haven't updated any firmware, but being a refurb unit I was under the assumption that it would be up to date. Perhaps not, though, as it shipped with an old Matter Control (v 1.3) and a 'Getting Started' video dated from 2015.
edit: firmware shows as ROBO3DR1PLUSV2 in Matter Control, which is the most recent I can find on the ROBO3D website.

Any idea about those loose wires in my original post?

 

Loose wires are on the left side of the machine

Additional pictures:
http://imgur.com/a/wgMPT

 

Thanks, wired it back up just light on the right side (red wire left, black wire right). Hope that's alright.

Does anyone else encounter that if they open Matter Contol, start a print, and then finish or cancel it that the manual control buttons for all three axes of movement are no longer responsive? I always have to restart Matter Control to regain movement controls.

I've also noticed that, no matter the situation, the Minus (-) controls for any axis - X, Y, Z - are never responsive until a positive movement has first been made, and then it will only allow me to move back as many times as I've moved forward. I'm assuming that this is just a safeguard feature to keep from damaging a motor or cracking the bed.

 

Mine is doing that also. My printer was dialed in for over a year, not having to do any adjustments, it was like heaven. Then one print the filament got twisted and it pulled the z up to the top and grinded away for I don't know how long before I checked on the print and stopped it. When I untangled the filament, the z crashed to the bed. I don't think it's a coincidence that since then I also couldn't go minus on any of the axis'. I haven't been able to get a good 1st layer for my life.