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Perhaps you could post links to these bookmarklets so we (and the Omni people) can better understand what they're doing. My guess, it would depend on how these "bookmarklets" are calling their pop-ups. Since they are probably using javascript window.open onload methods to do this, they will be treated as malware and blocked.

I would recommend contacting the authors of these bookmarklets and requesting they re-code in a way to not trigger a pop-up blocker, rather than re-engineering a useful and otherwise reliable pop-up blocker in the browser.