Thanks Richard and Bart for the reponses,
In the end I followed Richard's suggestion for downloading the data, and then used Moss (http://theory.stanford.edu/~aiken/moss/) for doing the matching. I used a simple (and ugly!) python routine to process the data:
import mosspy
m = mosspy.Moss(1, "matlab")
for question in range(11,16):
for submission in questionFilenames[question]:
m.addFile(submission)
url = m.send() # Submission Report URL
Cheers, Angus