Anyway, I think I posted that other message a little too soon. Even though my 'fix' allowed the homepage to load correctly, it caused other problems. So unfortunately it looks like we're going to have to find another solution.

For one thing my search wasn't working anymore. I guess it posted to index.php which didn't receive the values anymore. I also couldn't use the core Joomla SEF URLS in the form /content/category/5/74/86/.

But for the sake of completeness I'll outline how to do what I tried, let me repeat though that it doesn't work as I thought it did:
1. Go to the JoomSEF control panel.
2. Click on Edit/View SEF URLS
3. Click New URL
4. Where it says New SEF URL, put index.php.
5. Under Old URL put the address of the page you want as a home page, you can get this by disabling the SEF and visiting the page you want to use. It should be something like index.php?option=com_content&Itemid=86&id=22&task=view
6. In ItemID, put the corrresponding itemid, in this case 86.

Then I repeated the above process but leaving the New URL field blank (empty).


The developers obviously want to make it difficult to read their code which also makes it harder to debug and offer other solutions. My only option for today was to restore version 1.5.1 which was working fine. I was hoping to do the upgrade to improve the efficiency of the code.

I had the same problem after upgrading to 2.1 from 1.5. All my SEF urls would work except for www.mydomain.com or www.mydomain.com/index.php.

After reading numerous posts here and trying various .htaccess fixes I came up with a solution. I realised after looking at a debug of the site that the the component wasn't finding any result for:
SELECT * FROM jos_redirection WHERE `oldurl` = 'index.php' AND `newurl` != '' LIMIT 1

So, I just added two entries in the Custom URLS to redirect to my home page of choice, one with the New URL empty and the other with just 'index.php'.

I am not sure if that is an official solution but it worked for me.

As a side note, I think I am my problem was related to the fact that I'm not using the com_frontpage module as my homepage.