X servers use two schemes to copy text between applications. The first and the old one is the cutbuffer and the second one is the selection and both work differently. Recent desktop applications on linux use two selections. The Primary and the Clipboard. Windows VNC synchronizes clipboard with cutbuffer but not with selections and because the new applications does not support cutbuffer the server keyboard is never synchronized.

To overcome this problem you can use autocutsel as shown below.

Install autocutsel:

wget http://savannah.nongnu.org/download/autocutsel/autocutsel-0.9.0.tar.gz
tar -zxvf autocutsel-0.9.0.tar.gz
cd autocutsel-0.9.0
./configure
make
make install

Execute autocutsel to background process

autocutsel &

Everything should work now with clipboard support for copy/paste operations between systems.