Depends on the source of the increased noise I guess. The new filter and/or intake box could be less noise-isolating and allowing more of the valve/engine noise to travel up the intake trumpets. Or, the new intake box could simply be vibrating and producing noise (even when connected properly). Or, you might have a loose screw or something! But, if the filter is in place and everything is tightened properly and you have a proper seal overall, and if you like the sound, I wouldn't really care about the why part as much...
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