As a temporary workaround it's possible to just remove the parallels unity plugin.
WARNING: this breaks at least coherence, perhaps some other functions too. The workaround can be reverted by simply reinstalling the parallels tools.
Instead of running the parallels tools uninstaller on a console run the following command: (assumes that the parallels tools are installed)
cd /usr/lib/compiz && sudo rm libprlcompiz_0_*
This fixed my problem but if you reinstall the parallels tools it will break again.