I recently ran across a problem where VMware workstation where the vm-guest, in this case Ubuntu, would not boot. The error message that popped on screen was "VMware Workstation cannot connect to the virtual machine. Check permissions on the directory..."
Looking at the directory permissions nothing had changed and the permissions all appeared right.
The fix
This was actually pretty easy to fix, in the vm guest's directory, I deleted all of the .lck folders and also the .vmem file. If you are paranoid about doing that, just move them or don't empty the trash.
Once I did this I was once again able to start the VM as normal and directory structure repopulated.
Hope this helps, be sure to leave a comment and let others know if this worked for you.
**Update
I've now also seen this when starting a windows VM. The full error shown was "VMware Workstation cannot connect to the virtual machine. Make sure you have rights to run the program and to access all directories it uses and rights to access all directories for temporary files."
In this case I head read that others stated you need to reboot the workstation, but you dont just kill the following processes adn then restart vmware workstation.
