I suspect the profiler's UA detection code is confused by the way WebKit nightlies just run your installed version of Safari but linked to the newer WebKit framework. (Look inside the WebKit.app bundle: the binary itself is under 100Kb.)

Unless you have installed Safari 4 Developer Preview (available to any body with an ADC account), your WebKit.app User-Agent string will say Safari 3.x, with a nightly revision number. The exact same revision on a system with Safari 4 will have a different string, though. So it's entirely possible to have a newer version of WebKit running in an older version of Safari, and vice versa.

I think any nightlies since the DP was released in August _ought_ to be counted as Safari 4, but some may not be for this reason.