There is a feature coming with EG 4.3 to automatically clean up programming code. Otherwise, my suggestion for now would be to try first pasting the code into a text editor (like NotePad or TextPad) and then try pasting it from there into EG. If that doesn't work... I'm out of ideas. Others might have some additional insight!
What "other applications"? I don't have the problem in cutting and pasting from EMACS, Word, or Adobe in EGuide 4.2.
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