@Ovidiu: my experience is that the plugins you've mentioned do not work with Wordpress Mu.
@Kostan: I wonder if the plugin isn't just working. Perhaps it is taking a long time, but I would not be surprised with 25.000 tables.
You can check if the plugin works by making sure you don't get a PHP error (don't forget to check your php error log, especially when display_errors is off ;) ).
Also you can check if columns of tables are being transformed to their binary counterparts. You can check this by using mysql admin or phpmyadmin to check columns of tables and see if they have been transformed from their textual type to their binary counterparts.
From the README:
"After you have selected the tables for conversion and pressed the button *convert columns to binary counterparts for checked tables* the plugin will go through all tables and look for columns of the type: char, varchar, tinytext, text, mediumtext, longtext, enum and set. Columns of these types will be converted to their binary counterparts according the list below:
- char --> binary
- varchar --> varbinary
- tinytext --> tinyblob
- text --> blob
- mediumtext --> mediumblob
- longtext --> longblob
As you might have noticed the column types enum and set are not changed to a different type, instead the plugin will set those columns character set to binary."
If columns are being transformed I would like to ask you to let the plugin run for a while (transformation of a 250 tables database took me in total about 5 min, so yours could in total take approx. 8hrs).
I hope this helps.