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Can you post a link to a test page that shows the problem you're having?

Hey, thanks for answering. I solved the problem by replacing the default transitions by a custom one. Your plugin is the best, thanks for it.

I recently ran into the exact same issue. Another way instead of a custom transition to fix this is to use the cssBefore and cssAfter options like this.

$('#selector').cycle({
        cssBefore: { zIndex: 100 },
        cssAfter: { zIndex: 0}
    });