Phew! Thank you so much Chuck. I will not touch those config settings again. Actually, I'm going to go and back it all up straight away.
I have no idea about the relative links on the header so I assume that was put on by somebody else. Thank you for correcting that.
The mention of vB
here is where I made an assumption that was wrong. Use Integrated forum stylesheets?
If you use a forum like vB3 or Threads and want to use the intergated stylesheet option, choose Yes
Turning that on fixed all the colour problems so I went ahead and did the bad thing. The colours that were on it that I originally wanted to keep were fine with the old version, but crap with the new one. The dark colour on the thin borders were used for the background of large boxes. I couldn't read the text. It really needed to be changed.
Thanks for fixing it all up. Paying for two install services in two days would have been a downer.