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Hmm, that is odd. Try removing the line:

$customField1 = get_option("theme_logo");

And replacing the line:

elseif ( isset($customField1[0]) )

with the line:

elseif( is_page_template('templatnamehere.php') )

Replace templatenamehere with another template you have, just make sure its different from store.php ’cause thats already being used in the first if statement so you wouldn’t see any difference then. Its just for testing purposes so either create a test template and use that in the above elseif statement or use an other template you have.
See if that helps.