Upgraded from iWeb 06 to 08, and now web address and links don't work

Hi there,
I recently had the hard drive of my computer replaced and the Mac shop automatically upgraded iWeb 06 to iWeb 08, without asking me (and they also upgraded iPhoto)... I didn't think anything of it and went home. The next time I tried to update my website in iWeb I was asked a question that went something like did I want to upgrade or change or did I want to go ahead or something? I foolishly just said yes, whatever, and did my updates to my website. Then I used Transmit to upload my website files to my web site host. The web pages themselves still all look fine in Firefox, but there is one massive problem: when I type in my web address, which is www.*****.com, in Firefox, I'm told: "404 Not Found - The requested URL /Site/Home.html was not found on this server". When this happens, I've noticed that the www.****.com that I typed into the address bar now has changed to http://www.******.com/Site/Home.html.... If I delete the "/Site" bit from this new "address" my website comes up! If I then click on the link The Albadukes e.g., this page comes up fine. I then click on Links, and this page also opens up fine. However, if I then try to go back to the page called The Albadukes, it doesn't open! Instead, I get the 404 Not Found message again. Here, I've noticed that the writing in the web address box of the browser has changed from "http://www.***.com/The_Albadukes.html" (which works) to http://www.****.com/The Albadukes.html" (i.e. with a space between "The" and "Albadukes" - doesn't work...). If I remove the space and instead add an underscore, then the page opens! This kind of thing happens in different directions between different pages within my website.
<Edited by Moderator>
I realise the problems when upgrading to 08 and I wish it had never happened, but it did. So my question is: does anyone know if these link and web address problems can be solved, or should I just accept that the problems are due to the upgrade and instead just recreate my website in 08 (and hope that 08 will work OK on my computer...)? I am very very grateful for any help!!
Many many thanks,
Sofie

Hmm, interestingly enough it works on my MacBook fine...just a lot slower but that's because of ram size. I cannot figure out what's the problem with it on my iMac though.
I've gone into Quicktime and deleted any divx files associated with that and still nothing.

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