The following setting it turned on by default and may potentially be the cause of your issue. If you haven't turned it off in your own user preferences, you might want to try doing so to see if it resolves your problem:
// If true, the copy and cut commands will operate on the current line
// when the selection is empty, rather than doing nothing.
As the comment mentions, when this is turned on the copy and cut commands both pull the current line into the clipboard. If you intended to paste the contents of the clipboard onto an empty line and pressed the copy key instead, this setting would replace the clipboard contents with the current (empty) line, which sounds somewhat like what you're experiencing.
Note also that you can use
Edit > Paste from History (see the menu for the default key binding for your platform) in such a situation to get back the text that was previously in the clipboard, should you find this setting helps more than it hurts in the general case.