After our upgrade to the latest AIMS, we are now experiencing issues with the legend. There is issues within the legend on how the legend tree is rendering. (jxLib css issues I suspect) I've attached some examples of what they look like, but I don't know where in all the jxtheme.css files used in fusion where it needs to be fixed.
There is no way someone else isn't have the same issue. I need a resolution quickly as our map isn't wokring at the moment for users.
I've seen the exact same thing in our AIMS applications, we have since moved to AIMS2014 and issue is now resolved on FF and Chrome, but IE10 looks the same as your images.
I never did find an exact fix, but part of the css that you should be concerned with is LI.jxTreeContainer within the jxtheme.css file.
Sorry I couldn't be much more help with that.
I know in IE at least, the out of place checkboxes in the legend is the result of IE compatibility mode being activated.