There is some incompatibility between Xvnc and MATE's notification dock. None of the icons there are visible, although they are otherwise functional.
This was reported on the thinlinc-technical mailing list for Linux Mint:
I also tested it on Fedora 18 with the same results though.
The upgraded Xvnc no longer suffers from this problem.
Tested using MATE on Ubuntu 13.04, everything appears to work as expected. Closing.