When you paste plain text into Microsoft Publisher, the data may not assume the font that you're working with. One user reported that every time he pastes into MS Publisher, the data is inserted using the "Lucida Sans" font, instead of the font that he's working in.
A simple experiment (closing ClipMate, copying from Notepad and pasting back into Publisher) confirmed that ClipMate doesn't have any effect on the data - it's just the way that Publisher works. He was using Publisher 2000 (sp-3).