Booting in to a clean installation of Ubuntu 12.04 (Precise) with VMWare Tools installed I get a Could not apply the stored configuration for monitors error:
The solution is to remove monitors.xml from /home/<username>/.config.
To do this I opened a Terminal and changed the directory to .config:
I backed-up and then deleted monitors.xml:
cp monitors.xml monitors.bak rm monitors.xml
I rebooted for good measure – now VMWare Tools adjusts my resolution without errors.