This is how I expect it to work: I load a page and open the Web Inspector. It shows me any JS errors. If I reload the page, the Inspector also reloads and shows me the JS errors. Often it does work this way.
Sometimes, though, one some pages, when I reload the page, the Inspector clears and reloads like above, but the JS errors don't show up in the console (I do get a red indicator next to the JS file with the number of errors). If I close the inspector and reopen it, the errors then show up.
I have tried restarting Safari, restarting my computer, and reinstalling Safari. This is Safari Version 3.2.1 (5525.27.1).