Hi Byron, thank you for your reply.
I have a feeling this is a subject that may get asked a lot due to the MU and Wordpress merging together. If i can help i will certainly try and resolve it.
Well here goes...
unfortunately all the tables are missing when you look in the admin panel form a new user:
Database Info
Tables:
o wp_3_bwbps_images: Exists - was missing...update run successfully
o wp_3_bwbps_galleries: Exists - was missing...update run successfully
o wp_3_bwbps_layouts: Exists - was missing...update run successfully
o wp_3_bwbps_forms: Exists - was missing...update run successfully
o wp_3_bwbps_fields: Exists - was missing...update run successfully
o wp_3_bwbps_lookup: Exists - was missing...update run successfully
However, it looks like when i visit this page everything is updated. So whatever happens when you view this page fixes the problems. The 'mu-functions.php' is where new default scripts are activated when new blogs are created. i.e extra pages. BTW, my prefix as seen above is wp_, i just cant figure out why it wouldnt activate when a new blog is created. :-s