Is there anything logged in your LOGS directory?
Also, I doubt this would make a difference, but make sure that your "sideboxes/bootstrap/search_header.php" has a unique Sort Order variable, just in case there's some weird conflict there.
I did a test and turned off my "sideboxes/bootstrap/search.php" but I am still able to see my "sideboxes/bootstrap/search_header.php" load just fine.
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