Using version 0.4.6 as distributed in Ubuntu 12.10.
Copy a multiline text.
Open a new 2-way file merge
Paste the text in the left pane
Paste the text in the right pane
The first line is matched, the following are not, despite being identical
It's probably due to to the lines added when copying: https://sourceforge.net/tracker/?func=detail&aid=3613190&group_id=157784&atid=805206
Yes, this is duplicate of bug #18. I can reproduce this with default 0.4.7 install, but cannot reproduce once I copy over GTK 2.24.20 that has the fix for line ends conversion.