BoyGenius points to some sketchy evidence found in their browser logs that seems to suggest iPhone OS 3.1.3 and 4.0 are being used in the wild.
The reason we label this as “sketchy” is that the ability to fake user agents is trivial. Many browser add-ons let you simply type in whatever you would like into the “user agent” field that is being reported. In this case, we also found similar user agent strings in our logs, though they were not originating out of an Apple IP address, but instead out of somewhere in Florida. Little else can be said about the finding.
iPhone 4.0 would suggest Apple is prepping a major OS update. iPhone 3.0 was just released back in July. A full version number upgrade would indicate a major release update.