Solidoodle 3 y-axis "thumping"

I was running a large print last night. I stepped away for a few minutes, and when I came back it looked like the y-axis had slipped and malfunctioned. I could see a distinct spot where the perimeter shifted in the y-direct on the print for a few layers, but when I got to it, the extruder was stuck in a corner just extruding filament and making an odd noise. I shut it off to deal with it today.

When I turned it on today, the x and z axes worked fine, but the y-axis 'jammed' after about 20 mm of movement. It got to the point and just wouldn't go any further (while making a loud vibrating noise). I can move the extruder easily in the x and y directions by hand. I went through the calibration steps from the "True Circle Realignment Instructions" tutorial (it won't let me post the link...) It worked for about a second, and now it will move fully along the y-axis, but it makes a 'thumping noise' every couple of millimeters and it shakes violently when it 'thumps'.

Anyone know what I need to do?

EDIT: I went through the steps in the realignment instructions again and it seems to be working now. I'll leave this up in case anyone encounters a similar problem.

I think what the issue was is that the y-axis motor was too high, which meant the tension in the track was too loose. I lowered the motor and it seems to have fixed the thumping issue.