In templating-kit/pages/global/htmlHeader.ftl, conditionalComment is only used when listing the theme's css resources. It should also be used for css' configured at page-template-level, as well as for all js resources.

Here's an untested patch that should solve this. while writing the patch, I noticed that all <script> tags were enclosed in a <!-[if ! lte IE 6]><!->. I moved the closing tag for that specific script up, so it only encloses the first <script>. I'm not sure this was by design or by mistake. It'd essentially strip all scripts for IE older than 6, which is pbly not a bad thing, but would prevent the usage of other conditions for each script. This shows a technique to nest conditional comments, but I haven't tried it out: http://www.dynamicdrive.com/forums/showthread.php?17401-Nesting-IE-Conditional-Comments

As a side question - why does info.magnolia.module.templatingkit.sites.Site have a jsFiles field, but note cssFiles ?