Same problem here.
“Clip to DT” (version 1.1) seems to interfere with the extension “ClicktoFlash” (version 1.6.1). Disabling “ClicktoFlash” solves the problem: both the bookmarklet and the extension work as they should.
I had not much time to test this - but maybe it’s the solution…
Clip to DT is the only Safari extension I have tried, and it is transparent for me too. I had been using the Clip to DT bookmarklet, which was the “smoke” type Growl interface. When I upgraded Safari to be able to use extensions, I installed the Clip to DT extension. Then Clip to DT became transparent, and useless.
I uninstalled the Clip to DT extension, and the Clip to DT bookmarklet worked as before.
Is there a conflict between the bookmarklet and the extension? Or what?
In my case, I didn’t even know about the extension until the bookmarklet went sour. The extension actually seems to work, until I use the bookmarklet. Then both go bad. Closing and re-starting Safari fixes the problem, until I use the bookmarklet again.
Also, ClickToFlash seems to have nothing to do with it. The bookmarklet still messes up, no matter the status of ClickToFlash.