I think I have found a good way to reproduce the problem: ICAClient.

It does not seem to directly use lesstif/motif, however:

$ ldd /usr/lib/ICAClient/wfica
        linux-gate.so.1 =>  (0xb7f9d000)
        libXaw.so.7 => /usr/lib/libXaw.so.7 (0xb7f05000)
        libXt.so.6 => /usr/lib/libXt.so.6 (0xb7eb4000)
        libX11.so.6 => /usr/lib/libX11.so.6 (0xb7dc5000)
        libdl.so.2 => /lib/tls/i686/cmov/libdl.so.2 (0xb7dc0000)
        libc.so.6 => /lib/tls/i686/cmov/libc.so.6 (0xb7c62000)
        libXext.so.6 => /usr/lib/libXext.so.6 (0xb7c53000)
        libSM.so.6 => /usr/lib/libSM.so.6 (0xb7c4a000)
        libICE.so.6 => /usr/lib/libICE.so.6 (0xb7c32000)
        libXmu.so.6 => /usr/lib/libXmu.so.6 (0xb7c1c000)
        libXpm.so.4 => /usr/lib/libXpm.so.4 (0xb7c0b000)
        libxcb-xlib.so.0 => /usr/lib/libxcb-xlib.so.0 (0xb7c08000)
        libxcb.so.1 => /usr/lib/libxcb.so.1 (0xb7bef000)
        /lib/ld-linux.so.2 (0xb7f83000)
        libXau.so.6 => /usr/lib/libXau.so.6 (0xb7bec000)
        libXdmcp.so.6 => /usr/lib/libXdmcp.so.6 (0xb7be7000)

Anyway: use any ICAClient to connect to a windows server machine. Then copy something from, say, konsole (using right-click then "copy" so that is goes to the clipboard, not only the selection buffer) and try to paste in a Windows remote application - try notepad for simplicity. It won't paste.

However, if I go to console and use "xclip", it will work:

$ xclip
<My selection goes here>
<Ctrl-D>
$

Then I paste it ok to notepad or whatever.

Here are my klipper options:

[ ] Popup menu at mouse-cursor position
[V] Save clipboard contents on exit
[V] Remove whitespace when executing actions
[ ] Replay actions on an item selected from history
[V] Prevent empty clipboard
[V] Ignore selection %

Clipboard/Selection Behavior
(*) Synchronize contents of the clipboard and the selection %
( ) Separate clipboard and selection

Timeout for action popups:
8 sec

Clipboard history size:
24 entries

I tried to change the options marked with % to see if it would work to no avail.

kdebase:
ii  kdebase-bin                                4:4.1.3-0ubuntu1~intrepid1                           core binaries for the KDE 4 base module
ii  kdebase-data                               4:4.1.3-0ubuntu1~intrepid1                           shared data files for the KDE 4 base module
ii  kdebase-runtime                            4:4.1.3-0ubuntu1~intrepid1                           runtime components from the official KDE 4 release
ii  kdebase-runtime-bin-kde4                   4:4.1.3-0ubuntu1~intrepid1                           core binaries for the KDE 4 base runtime module
ii  kdebase-runtime-data                       4:4.1.3-0ubuntu1~intrepid1                           shared data files for the KDE 4 base runtime module
ii  kdebase-runtime-data-common                4:4.1.3-0ubuntu1~intrepid1                           shared data files for the KDE 4 base runtime module
ii  kdebase-workspace-bin                      4:4.1.3-0ubuntu1~intrepid1                           core binaries for the KDE 4 base workspace module
ii  kdebase-workspace-data                     4:4.1.3-0ubuntu1~intrepid1                           shared data files for the KDE 4 base workspace module
ii  kdebase-workspace-libs4+5                  4:4.1.3-0ubuntu1~intrepid1                           libraries provided by the KDE 4 base workspace module