When your students use JavaWIDE, you may notice some peculiarities in the way that copy/paste works differently sometimes. This is due to the fact that there are actually two different clipboards - an internal one and a system one. Unsigned java applets don't have direct access to the system clipboard which is why pasting with ctrl-v and selecting the paste menu option has different results sometimes. The ctrl-v always pastes from the system clipboard and the menu option always uses the internal clipboard. Sometimes these are the same and sometimes they are different. For more information, see
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The bottom line is that you should teach your students the keyboard shortcuts for cut/copy/paste. These are ctrl-x for cut, ctrl-c for copy, and ctrl-v for paste. Not only are these keyboard shortcuts usually faster than the menu options, but they also make the cut/copy/paste experience consistent. These shortcuts also work in other applications so your students are learning transferrable information.
Note: even on Macs, use ctrl-x, ctrl-c and ctrl-v for cut/copy/paste within JavaWIDE. On the mac you'll need to use COMMAND-X, COMMAND-C, and COMMAND-V outside of JavaWIDE for cut/copy/paste.