Dijkgraaf - 12:20 am on Dec 20, 2011 (gmt 0)

Those /?DA etc. look like corrupted directory sorting options for Apache.
?M=D sorts the directory by last modified date, descending.
?D=A sorts the directory by file description, ascending
?S=A sorts the directory by file size, ascending
etc.

And by what you've said so far, I'd say Google is getting a directory listing.
So you either
1) need to change the settings on your sever so it disallows directory listing.
2) Put redirect rules in place.
or 3) or put an index page in each directory with a either with canonical url or that issues a http 410