This may not help you resolve the issue (I'd recommend opening a support request with BMC). However, I'd be curious if the copied content is being coppied over as HTML content (HTML or rich text) or as plain text.
I'd be willing to bet, without testing, that the content is being copied as html content. HTML content can have a mind of it's own and may overwrite the simple HTML editor in FootPrints.
Just a thought.