Ok, I've changed everything back and it seems to be working again, but with the incorrect stats because it's missing the maildir space used.
The only things i've changed back are :
config.inc.php changed the use sudo option to a "0" again instead of 1
config.inc.php changed the encryption back to crypt from md5
visudo removed the admispconfig line added from the initial settings howto
Kinda stumped why any of those would affect it, but it would seem that ispconfig can't get the files diskspace used as they are not even listed, only the mysql space is listed before I changed those settings back. Now all the folders are listed again.
Thanks for any suggestions from anyone who's done this.