Based upon that it sounds like some geolocation problem.
The vanishing index/home page syndrome that I've seen reported in various forums for the past nine months shows some unique components. The page can be accessed in Google but it won’t appear with any direct phrase or keyword search from the page. This is consistent across all Google country engines and DC’s. The other pages of the site are seldom effected. Another aspect of this syndrome seems to be the index/home page is skipped over in the initial keyword or phrase search but will appear if you click on “more results from www. mydomain .com". I was trying to explain how to do this to Zeus.
If you can access the index/home page through any long-tail search you aren’t suffering from this vanishing index/home page syndrome. In those cases likely you have fallen victim to Google’s newer quality control features or the 950 penalty. I believe the new quality control features have some aspects exported from Adwords and do utilize manual reviewers.
Robert and Tedster though both present a clearer view of the problem and the things you need to look at first on your site that may explain your troubles before you consider this. This penalty seems to effect an aged site which has made some recent changes. From what other people have shown me nothing really black hat.
Bottom line though is many index/home pages are presently highly volatile in Google without any penalty. I believe this particular penalty though came from the de-emphasizing of the index page in all Google searches. Google was trying to elevate the sub-pages of many large sites that dealt in a variety of subjects. Basically you have to kill one to emphasize the other or vice versa. In my mind two different levels of optimization can't really co-exist in many cases. It also may deal with the way Google crawls now.
I call it a penalty because it has a definable exclusionary effect whether intended or not by Google. A thinner wallet is sufficient evidence for me though.