I’ve just been struggling with the same issue and managed to get it to work with rewrite rules in the web.config. I basically copied those which KuroTsuto supplied the tinkered with them until I got them to work.
These are the rules that work for me (added before the WordPress ‘Main Rule’ rule):
<rule name="w3tc_rewrite_test" stopProcessing="true">
<match url="^wp-content/cache/minify/000000/w3tc_rewrite_test" />
<action type="Rewrite" url="wp-content/plugins/w3-total-cache/pub/minify.php?w3tc_rewrite_test=1" logRewrittenUrl="true" />
</rule>
<rule name="w3tc-minify-test-file" stopProcessing="true">
<match url="wp-content/cache/minify/(.+/[X]+\.css)$" />
<action type="Rewrite" url="wp-content/plugins/w3-total-cache/pub/minify.php?test_file={R:1}" />
</rule>
<rule name="w3tc-minify-file" stopProcessing="true">
<match url="wp-content/cache/minify/(.+\.(css|js))$" />
<action type="Rewrite" url="wp-content/plugins/w3-total-cache/pub/minify.php?file={R:1}" />
</rule>
