A couple of days ago www.mysite.com appeared to have been dropped from SERPS for my common search string however www.mysite.com/index.php is showing but much lower down the list.
The home page has an item randomly pulled from a database each time the page is accessed- I seem to remember reading that this could cause a problem with a bot going back to the page and finding that it has changed.
Has this caused my problem?
I can't see why www.mysite.com isn't being listed as all external links point to that url though internal links do point to www.mysite.com/index.php
though internal links do point to www.mysite.com/index.php
That's why. When Googlebot sees a link to www.mysite.com, it indexes that and drops the other one for duplicate content. Then when it sees a link to index.html, it indexes that one and drops the other.
I don't know why they wouldn't rank the same. But on internal links, you can link to "/", and it'll be the same as linking to www.mysite.com.