Very quickly:

Using ZenCart 1.3.9h
Using heavily modified All Business template
Using custom buttons and changed them from .gif format to .png
(not sure if this is relevant, but I might have screwed up a function while doing so, unlikely but still...)

So...

I would like to use the CSS search button on the header when CSS buttons is turned off globally.

I went into a
/includes/templates/YOUR_TEMPLATE/sideboxes/tpl_search_header.php

and changed the code by commenting out the lines for the altnernative when (IMAGE_USE_CSS_BUTTONS) == 'yes') in the if/else statement

and replaced it with a duplicate lines of when (IMAGE_USE_CSS_BUTTONS) == 'yes')

therefore logically the CSS button would be used in the search header if CSS buttons was turned on or off globally

Code:
  if (strtolower(IMAGE_USE_CSS_BUTTONS) == 'yes') {
    $content .= zen_draw_input_field('keyword', '', 'size="6" maxlength="30" style="width: 100px" value="' . HEADER_SEARCH_DEFAULT_TEXT . '" onfocus="if (this.value == \'' . HEADER_SEARCH_DEFAULT_TEXT . '\') this.value = \'\';" onblur="if (this.value == \'\') this.value = \'' . HEADER_SEARCH_DEFAULT_TEXT . '\';"') . ' ' . zen_image_submit (BUTTON_IMAGE_SEARCH,HEADER_SEARCH_BUTTON);
  } else {
	$content .= zen_draw_input_field('keyword', '', 'size="6" maxlength="3" style="width: 100px" value="' . HEADER_SEARCH_DEFAULT_TEXT . '" onfocus="if (this.value == \'' . HEADER_SEARCH_DEFAULT_TEXT . '\') this.value = \'\';" onblur="if (this.value == \'\') this.value = \'' . HEADER_SEARCH_DEFAULT_TEXT . '\';"') . ' ' . zen_image_submit (BUTTON_IMAGE_SEARCH,HEADER_SEARCH_BUTTON);
    //$content .= zen_draw_input_field('keyword', '', 'size="6" class="search-header-box" maxlength="30" style="width: 150px" value="' . HEADER_SEARCH_DEFAULT_TEXT . '" onfocus="if (this.value == \'' . HEADER_SEARCH_DEFAULT_TEXT . '\') this.value = \'\';" onblur="if (this.value == \'\') this.value = \'' . HEADER_SEARCH_DEFAULT_TEXT . '\';"') . '&nbsp;<input type="image" src="includes/templates/all_business/buttons/english/button_search.gif" value="" class="search-header-button" style="width: 75px" />';
  }
did not work, it would display the .png image button in it's place which is very strange because I hadn't even modified the original code to point to the .png file

before commenting out, I tried (IMAGE_USE_CSS_BUTTONS) == 'no') same result.