Clipboards in Unix work differently than in Windows. The main clipboard, called the primary selection, in Unix (X11, really) is basically whatever is currently highlighted. If jEmplode highlights something for you, you lose what was previously selected. This is the clipboard method used 99% of the time in Unix/X11. There is another clipboard that works largely like the Windows clipboard, but it's so underused that many applications don't have any way to access it at all.

This is obviously a place where jEmplode running under Unix should behave differently than jEmplode running under Windows. (For the record, MacOSX works more like Windows in this regard.)