I'm not having much luck with this (otherwise very promising) plugin. Could this be the problem:
You call jQuery.browser.msie && jQuery.browser.version<=6 to test for IE 6. jQuery.browser. is deprecated (but might still work). In addition, jQuery.browser.version appears to return a string, with a format that can vary by browser. To compare numerically, follow the example parseInt($.browser.version, 10) (see the jQuery API).
I hope this helps improve the next version of your plugin!
UPDATE: At this point, I can't get ANY IE warning plugin to work, so maybe this plugin works just fine and my testing is bad. ... Can anyone else confirm/deny this plugin works?
http://wordpress.org/extend/plugins/shockingly-big-ie6-warning/