I recently release Beta 2.5 of DnaFamilyTreeBuilder, and this was a feature added to it. It also creates the mother of all cross Matrix -- i.e. it will automatically download all of the Matrix data and then create a super matrix showing all in one Excel (CSV) file.

I did 182 x 182 with no problems (does take a minute to do). It also supports the import of 23andMe data and will produce a matrix of it's data.

http://dnafamilytree.wordpress.com/

For information, examples and link to download.

It's free and it's beta software.