I know it's not the best thing to mess with especially the jquery but i have been using the async jquery plugin to move it to the bottom and load async.
But when i disabled this plugin, it pulls the jquery off my site. Initially i thought it was just the async plugin causing the problem, but i have since tested it with my other site which have other plugins.
I reproduced my steps by activating this plugin, and proceed to disable all my other plugins. The jquery is still there, until i disable this one.