Gaps while printing with Mini (not from under extrusion)

[CPS]

My Makerbot Mini has been leaving parts of the print out. I've attached a couple of examples of this occurring:

IMG_0011.jpg IMG_0012.jpg
The first image is the one with the problem while the second is what it should be looking like.
IMG_0013.jpgIMG_0014.jpg


While watching it print, I noticed that upon reaching a section that it misses out, the extruder moves upwards about 0.5cm and it stops extruding any plastic. It then moves along horizontally until it reaches the end of the missing section and then moves back down and carries on as if nothing happened. As can be seen in the images, it happens multiple times in the same X-Y position with different layers. This has happened a couple of times now with completely different models (it has happened on both straight lines and curved lines too).
After looking through some 3D printing troubleshoot guides, I haven't seen anything similar to this. Has anyone had a problem like this or maybe even know of a way to fix it?
I was thinking it might be a software problem with the way the extruder purposefully avoids the area. If it makes any difference, I use 123D Design to create the objects and export them as an .stl file and then print using makerbot desktop.

[GOC]

- Question: Are you using the same GCode or are you re-crunching the code for each machine? Its consistent misses makes me think it could be bad slicing.

- If you could attach the GCode File(s) I could examine this issue further.

[CPS]

I thought Makerbot 5th Gen stopped using g code and now uses the .makerbot file extension?

I've unzipped the .makerbot file and found the .jsontoolpath which I assume is the makerbots gcode equivalent?
Is this useful to you at all?
The file is about 39MB which is apparently over the limit for .txt attachments. I've put it in a .zip file if that is ok.

print.zip

[wackyvorlon]

They haven't run g-code for quite some time.

[CPS]

They haven't run g-code for quite some time.

Do you know if it is possible to read the file that makerbot now uses instead of g-code in a similar way to g-code?