I am using the latest Atahualpa and also wp 3.1.1.

When I install the Magic Gallery plugin it works fine in Firefox but in Internet Exoplorer the shadowbox slideshow fails and clicking on an image in the gallery just opens the picture in a new window.

An error shows at the bottom of the page which says that prototype.js and jquery.js are not supported.

Alan

This sounds like an IE issue. Do a google search of 'ie prototype.js and jquery.js'

Your right - Having spent all day changing thing to identify the conflict which got worse locking up the widget page in the dashboard etc.
I discover that in IE8 there is a "Compatibility Mode". Switch that on and everything is fine.

The issue only seemed to affect Atahualpa 3.6.4 and Wordpress 3.1.1 combination but then I was getting a bit punch drunk and being just a simple country boy more investigation was passed my skillset.

Alan