I think there may be some conflict between WP Super Cache and the WordPress Mobile Edition plugin by Alex King.
I got a call from someone yesterday telling me that my home page looked very strange but that other pages on the site were fine. I checked and indeed, the Mobile Edition was loading on just the home page. I remembered that I had checked the home page from my phone earlier that day and so I cleared the cache and lo and behold the front page loaded fine.
I cleared the cache again, but this time browsed to the home page from my phone (it showed the mobile version as expected). On return to a normal browser I loaded the home page and once again the mobile version was showing.
For the time being I've just disabled the mobile version as it's not really crucial for us, but I can imagine a few people would find it very necessary.
Of course, I don't know whether this is something that needs to be adjusted on the Mobile Edition end, or on the Super Cache end, but thought I'd give you a heads up anyway.
If there's any test you need run, let me know.