Have you tried disabling server compression for IE? I don't know why, I've met this error before and this fixed it for me:
RewriteEngine on
<IfModule mod_headers.c>
RewriteCond %{HTTP_USER_AGENT} MSIE\ [56]
RewriteCond %{HTTP_USER_AGENT} !SV1
RewriteCond %{REQUEST_URI} \.(css|js)$
RewriteRule .* - [E=REMOVE_IE_ACCEPT_ENCODING:1]
<LocationMatch \.(css|js)$>
RequestHeader set Accept-Encoding "" env=REMOVE_IE_ACCEPT_ENCODING
</LocationMatch>
</IfModule>
Basically modifying headers for Accept-Encoding.. but I can't find my notes on disabling compression for IE though. It's a good place to start nonetheless. Sometimes it's the optimizations that bite us in the ass.
EDIT:
After digging a bit, here's for disabling compression: http://www.aptivate.org/webguidelines/EnablingCompressionOnYourWebServer.Apache2.html