Attached is a fix for this bug.  Also here is a link to the bug report at the 
synergy2 project.
http://sourceforge.net/tracker/index.php?func=detail&aid=2033712&group_id=59275&atid=490467

To apply the patch:
1. tar zxvf synergy-1.3.1.tar.gz
2. cd synergy-1.3.1
3. patch -p1 </tmp/synergy-1.3.1-64bit_bug.patch


** Attachment added: "fixes clipboard problem on 64bit systems."
   http://launchpadlibrarian.net/16450827/synergy-1.3.1-64bit_bug.patch

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ClipBoard not working with java (swing) applications
https://bugs.launchpad.net/bugs/207057
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