We've had issues with Klipper immediately stealing the clipboard whenever it gets updated from the server. This can result in incorrect contents, and even non functional clipboard in either the client or server.
And fix upstream:
Apparently this was a general Qt bug that would affect any application using that toolkit. A workaround was possible in Xvnc though.
Verified that I could reproduce the problem with interfering klipper using ThinLinc v4.9.0. Upgraded to nightly build and there is no apparent interference with klipper and clipboard.