Multisite Broken Pagination

Hi everybody.

I´m running a wordpress multisite buddypress installation with over 200 sites for my university.

The problem is that after the latest update category pagination broke down and I have not been able to fix it yet but time is getting short so help is desperately needed.

The thing is:

Multisite, permalinks /%category%/%postname%/ structure
For category listings y get the first page Ok but the second one would show an 404 iin any of the sites.

Example

http://www.farq.edu.uy/publicaciones/libros/ works ok!
where publicaciones is the site and libros is the category.

fine…

now´s where the problem shows up

http://www.farq.edu.uy/publicaciones/libros/page/2/ would show a 404

strange thing is if I force the URL and point my browser to:

http://www.farq.edu.uy/publicaciones/page/2/?cat=libros
http://www.farq.edu.uy/publicaciones/page/3/?cat=libros

it would work perfectly fine

any help on solving this issue form my entire site would be much appreciated.

thanks in advance,

andrés