No… I managed to click on it and accept before it when away. It took be a lot of attempts, but I managed!! So it doesn't show up away anymore when I clip sites with DEVONThink.
But basically the problem is that small windows that is asking you "do you want to allow this page to open 'DEVONThink 3'?" disappears away really fast. Like perhaps 1 sec or so…
If you manage to click on "[ ] Always allow 'clip' to open this type of links", the windows doesn't appear anymore. However, as I said before, this is really challenging.
I think the problem is that after the window appear, something triggers the page to reload. For that reason the windows disappear. That happens with all kinds of pages… wasn't one in particular. I tried different ones with the same result.