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I have figured out the behavior a little further. I have a bugmenot bookmarklet in the position associated with Command+3. When I click on it normally in sp17, it gets blocked. In order for it to appear in a new tab, besides Command-clicking it, I have to hold Command after releasing 3. If I press Command+3 and release Command immediately, the bookmarklet registers "normally" and gets blocked.

I agree with nelio that this is improper behavior and bookmarklets should never be blocked. I believe they are "requested" popups and should be bound to the preference that popups are only blocked when not requested.