Any nightly build including and above r24668 seems to break SafariStand's ability to block all plug-ins. Normally with the 'load plug-in manually' feature of SafariStand enabled, Safari will render Flash and other plug-ins with a gray box enabling the user to click to manually load the plug-in. Any revision of WebKit after r24668 just runs all plug-ins regardless of SafariStand.
Thanks for the bug report, Nathan! Unfortunately, SafariStand (and similar add-ons) rely on internal WebKit APIs that are not guaranteed to stay the same. Please report the issue to SafariStand, although my guess is that they won't update their plug-in just for nightly builds.