Looking at admincp/template.php in the "if ($_POST['do'] == 'updatetemplate')" section (around line 2236), it looks like if you are changing .css templates you need to call build_style() after (in includes/adminfunctions_template.php). Also if you change a template starting with 'bbcode_' you need to truncate the 'postparsed' table (but I'm guessing that's not part of the problem you're having).
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