Filament Bunching Inside Acrylic

I think this is normally caused by clogging in the nozzle from overheating or misalignment of the PEEK relative to the jigsaw or by heat traveling up the filament and softening it to the point that it is easier to bend than extrude. 

Misalignment and clogging can be checked by simply disengaging the idler bearing tension and manually pushing to extrude plastic.  If it feels relatively easy, I would think it could be softening, and I'd try printing colder.

I print ABS at 190-195, but I haven't heard of deteriorated plastic causing clogging at 200 unless there are additional causes like too much backpressure because the nozzle is too close to the bed or the flow rate is too high like you're wondering, but in those cases, I usually see the drive gear digging into the filament and lose traction before the plastic would bend like that.

Since you can get 30 minutes of printing, I would check calibration as per http://wiki.solidoodle.com/flow-rate .  If it's high, then yes, your putting too much through.

Not being too patient, I'd probably try switching out the nozzle fairly quickly to see if that fixes the problem and dump the old one in acetone for a week.

If you're sticking the guitar wire and coming in from underneath, one could imagine a clog being dislodged and then reclogging once the wire is removed, but not having experienced it, I would think extended overheating would cause filament to build up on the nozzle like artery plaque, and that would keep building up after guitar wire cleaning.  How clean is the filament and room you're printing in?

Filament quality can definitely play a factor, but I've never used Solidoodle's own plastic so I don't know how good it is beyond several people going with it since it is the same vendor as the machine itself.  I've gone through about 20 spools and I have an assortment of about a dozen colors spread across 4 brands, and I notice few differences and only a 5 degree spread in optimal running temperatures, but others have reported more spread.  I've had two bad spools total and those had that effect I mentioned of the drive gear digging into the plastic issue.

It sounds like a good idea to try .3mm for a bit, but I don't see why .1mm should be a problem with a well-leveled printer (I typically print at .3mm but it's because I print a lot and need speed and do acetone finishing for smoothing).

Morty, this is ABS, right?

I had a very similar problem when my temp defaults kept switching to 195 when printing PLA (should be 180)

Even if it is ABS, I'd bet it is still a temp problem. You might chech the high and low temps you are cycling through at 200.

Yes, it is ABS. I know it is sacrilegious, but I live in NY and work right down the street from the Makerbot store. They have a big selection and I don't have to wait for shipping. I can't imagine that their quality control is poor, but if someone has had a bad experience with this brand with the SD3, please let me know. As for the room I'm printing in, it's an office with a few computers in it so I can't imagine it's too dirty.

I was going to put an enclosure on my SD3, but I would imagine that this would make the problem worse. I think the first thing I will do is swap the fan out and print at 190. I've had nothing but issues with the fan, starting with the connector being installed backwards straight out of the box. I didn't even notice it wasn't running until the second test print. After I contacted support, they told me to flip the connector around. It must happen often enough for them to suggest that. If that doesn't work, I'll try a new nozzle per Fred's recommendation. Thanks to all for the suggestions. I'll keep you posted as to what I find. It's a bit frustrating as I've had the printer for two weeks and have not made it completely through a print yet due to various problems. Admittedly, some of the issues were due to the learning curve.