Well Guys,
I have gotten around my problem, not sure how much it will help you but I'll let you know just in case. It might perhaps help someone else too who is setting up KnowledgeTree.
I removed the RPM for KT3.1 with rpm -e and then manually deleted the MySQL DMS KT database by using the sme-phpmyadmin rpm (I know I should have used the command-line for this but was feeling lazy).
I then just created my own Docs iBay, dumped the knowledgeTree files in there with the right permissions, set up the DMS MySQL databse again and used this post as a reference to allow .htaccess in the iBay to work and to set up the bay for knowledgeTree;
http://forums.knowledgetree.com/viewtopic.php?t=1321&highlight=smeThen the rules in the .htaccess in the Docs iBay came into effect successfully.
For those who are setting up KnowledgeTree and having trouble setting up the catdoc, pdftotext paths etc, then by first installing the VanHees KT rpm and following the instructions on the original post here;
http://forums.contribs.org/index.php?topic=34229.0and then removing the RPM as I mentioned above I got myself the latest version of KnowledgeTree (3.3.2 instead of 3.1) after following the instructions at the top of this post! I know this is an extremely long-winded way of doing it but it just worked for me!
bpivk has reported that he is currently updating the sme-knowledgeTree rpm to the latest version but will be a while yet.
Hope that is of help to someone.