Not 100% sure if this is a bug, or a new feature and maybe there's an option to disable or alter its behavior:

When a jQuery modal dialog window pops-up, the greyed-out/disabled area is no longer the whole background screen, there is now a line about 1 inch high that spans the entire screen from left to right behind the dialog.

Is there an option to turn this off?

This bug only seems to happen in IE, when you click a element it jumps to focus to the top of the parent element this is however a bug as for example if you have a small work area (800x600) it'll move the clicked element out of view which is obviously not a desired behaviour. It should probably focus on the clicked element or do as firefox and just not move out of view of anything.

The _checkOffset function uses clientWidth and clientHeight of document.documentElement to get the dimensions of the viewable window. The proper method to use in Firefox is innerWidth and innerHeight of window.

For example, on a sample page I made the following was returned

console.log(document.documentElement.clientHeight);	// returned 295
console.log(window.innerHeight);			// returned 617

This actually caused the dialog to pop up above the input box even though there was plenty of vertical space available.