It can be possible that if you list your homepage in a specific way & if google finds it as spam or keyword stuffing it would not index your page or may you should wait for some more time to have next google update.
Yes, It can be reason also. You should check your website contents that its duplicate or unique or keywords stuffing or not etc.. and write contents and put keywords according to search engines rule.
Submit your sitemap to google.
I think these would help you lots.