IE 11 does not support conditional comments.
Conditional comments are no longer supported
Impact Applies to Internet Explorer 10 and later. Affects IE10 Standards mode and later, including interoperable quirks mode. Support for conditional comments has been removed in Internet Explorer 10 standards and quirks modes for improved interoperability and compliance with HTML5. This means that Conditional Comments are now treated as regular comments, just like in other browsers. This change can impact pages written exclusively for Windows Internet Explorer or pages that use browser sniffing to alter their behavior in Internet Explorer.
You'll need to try another way to target IE11 specifically.
Searching around SO brought me to this answer, which uses feature detection to determine whether or not to load Polymer's polyfills.Searching around SO brought me to this answer, which uses feature detection to determine whether or not to load Polymer's polyfills.
