Any idea why it is being stripped? rebuilding the post cache just means reparsing posts, if they displayed data before they should do so again.
Having said that they "fixed" a "problem" in 3.6.6 where by empty tags are completely removed from both the parsed and raw text. If your custom tags are empty then they will have been removed.
To prevent this behaviour edit includes/class_dm.php and comment out the line
$pagetext = $this->strip_empty_bbcode($pagetext);
which appears in function verify_pagetext.
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