[ubuntu] Does the Clipboard not copy from Java based programs?

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http://ubuntuforums.org – I'm a huge Arduino (microcontroller programming) fan, I noticed today that at times when I copy from the Java based Arduino that I can't paste into GEdit... BUT I can paste back into another Arduino window. But the opposite works. I can copy from GEdit and paste into the Arduino Compiler. Curious why this could be? (Hardware)