Compared the code in the twentyeleven theme and the etcl theme that is generating the links on the pages. The code is different, but the output from each is identical (other than the order of the attributes), so I'm not sure why the navigation fails. I guess the ETCL theme must parse the arguments in the URL differently than the twentyeleven theme does, but that doesn't make sense, as that would be the DB doing that parsing and it hasn't changed.
TwentyTen theme
Brown Bag Seminar: Close Reading, Distant Reading and in Between
http://hcmc.uvic.ca/~etcl/wordpress/blog/2012/03/13/brown-bag-seminar-close-reading-distant-reading-and-in-between/
ETCL theme
Brown Bag Seminar: Close Reading, Distant Reading and in Between
http://hcmc.uvic.ca/~etcl/wordpress/blog/2012/03/13/brown-bag-seminar-close-reading-distant-reading-and-in-between/