Hey all, many thanks to BenBE who spent a long time fixing this with me on IRC. There were several issues but it seemed to boil down to having incorrect crypted passwords in these files:
/var/www/ispcp/engine/ispcp-db-keys.pl
/var/www/ispcp/gui/include/ispcp-db-keys.php
/var/www/ispcp/engine/messager/ispcp-db-keys.pl
By blanking the DATABASE_PASSWORD in /etc/ispcp/ispcp.conf and running /var/www/ispcp/engine/ispcp-db-passwd we were able to change the password, we then needed to make sure all the files above had the same crypted password in, as well as /etc/ispcp/ispcp.old.conf
Other issues were relating to FCGI, specifically the MaxRequestsPerProcess configuration directive in /etc/apache2/mods-available/fcgid_ispcp.conf - being as I am on Etch this directive caused an error so it had to be commented out.
Finally, the /var/www/fcgi/master folder was not present, so we were able to remake this from a domains folder by changing some values, and also my vu2000 user and group were gone, so they had to be remade by altering the user and group files (and shadows).
All seems ok now