Currently using:
Makerbot Rep2
Sailfish v7.7
A combo of ReplicatorG and Matter Control (Also tried Makerware)
Usual temp of 200C, have tried with 210, 220, 185, 190, 195
PLA
Mods include glass build plate (Makerbot) Spring loaded extruder design (Makerbot) New Thermocouple (Was also doing it with the old one, but got a new one anyways, old one was breaking. Can't remember source, but it has a nice cloth coating on it, and a nice rubber terminal on the hex screw in portion)

Every time i print, it starts out great. Perfect. But then, at some point throughout the print (It always gets minimum of 5-10 layers down) it simply stops extruding. No matter how hard i try to push it while it prints, nothing comes out. The extruder stepper keeps spinning, the cog/drive gear isn't spinning on the axle, and if i pull out the filament, it has obviously been ground away. With that, i highly doubt its the extruder (But maybe it is?? A new drive gear, Makerbot, is on the way.) If i immediately pause the print, i can run the change filament command, hit load, and give the filament a nice big push, it comes out again without any problems. Occasionally, i have to do the unload first, snip off the end, and then do load. When i unpause, however, two things may happen: 1, it prints a few more layers, and issue occurs again. 2, it doesn't print at all.
It did this before I upgraded to Sailfish. It did this before changing the thermocouple. I have tried Mattercontrol, Replicator G, and Makerware as slicers. All with the same outcome, more or less. Tried all of the above, with temps ranging from 185 to 225, stepping by increments of 5. Why?? I have been working on this piece of equipment for the past 4 days with no avail. Why does it do this? How do i fix it? If any more info is needed, just ask.
You can also send x3g files to me to test print.
Pictures:
http://imgur.com/a/Ler7W
http://imgur.com/a/OQorA
http://imgur.com/a/tGjqy

Thanks