Heres an odd thing.
I have a fairly bare 'splash style' index page with about 10 links to my most important internal pages and a graphic.
On my 'main' internal page I have links to another 80 of my pages, just like on my site map, and those pages are interlinked where relevant.
A week ago I added those other 80 internal links to my index page, freshbot came around, and a day later the www was missing from my index page listing, and it only showed up for 1 primary key phrase based on my domain name. The fresh tag was gone too, and the cache date was over a week old.
Doing a site: command showed my index page listed WITH the fresh tag, www, and recent cache (with all the new links).
I removed those links, and 2 days later, everything was back to normal. A few days later, I added the links again, and the exact same thing happened. I took them down, and back to normal a couple of days later.
I think I'll leave the index page as it is for now!