Tom,
I think Steven is on the right track. When CE doesn’t respond, it’s usually because Windows has decided you want the focus to be somewhere other than the active chart window. That is usually related to whatever you clicked on most recently. To get the Windows focus back to CE, just click anywhere in the active chart window. Then click again to get rid of the annoying property box that CE assumes you wanted. After that, Windows will again feed your keyboard input to CE, and your X will work as you intended.
After a while, you get used to feeding CE a couple of clicks every time you do anything outside the chart window.
You can also put a Reset XTE button on the instrument panel. Or, when you put the Route Monitor instrument on your panel, you get a Reset XTE button under the cross track indicator. If I remember correctly.