I'm having a similar problem... I'm trying to load extra .js scripts in my theme but 2.6 adds jQuery to the very bottom of the head... all calls to jquery in scripts included in the head of site.master fail as they are out of order in 2.6 now. In 2.5 we
could just include the js scripts in the theme name folder and they were added after jquery.
The only way I can get it to work in 2.6 is by adding the scripts to the body instead of the head.
I suspect that's the problem with the post above as well... (his call to jquery.snowstorm.js failed without him adding jquery above it as blogengine now puts it at the very bottom of the head). I'm not thinking it has anything to do with with IIS or
We need a way to add the script to the theme name dir and have it load below the jquery... I would think this version would break any lightbox script etc. that relied on jQuery to be loaded first.
Any ideas how to get around this besides adding the scripts to the body?