All my other pages have remained the same PR2 , but my home page when loaded without domain.com/"index.php" shows up as PR0 now . Once I click the link that directs back to "index.php" PR2 shows up again. Any idea what's going on? thank you
Try to get strong backlinks to your homepage and also point other inner pages which has PR to the homepage.
google see domain.com and domain.com/index.php As different pages So thats why you have different Pr on your main domain and landing page
Promote your site using your index page ex:www.index.com ,...and don't you worry about your PR it will come back again just continue to promote it.
Are you selling dofollow text links on your home page ? If you're doing so, then it's normal and happens once your website gets reported to G However, normally it won't affect your website ranking and you PR will never recover unless you get rid of those links and request a reconsideration from Google
from .htaccess file check the code of non www to www conversion, google might confuse in that for your site and get more back links for home page ( means your domain name ) not submit index page.
Its also possible that the dataservers holding your info are down at the moment. There are days my site has PR3 then reverts to PR5
If you could, then use redirect on your homepage from any possible variations into that one that has PR.