When troubleshooting the X server, remember the key components that make up the windowing environment. The X server must be able to start before the window manager and desktop managers take over. Take note of the X server that you are dealing with and check the documentation that comes with the version. The documentation located under the /usr/X11R6/lib directory contains examples including options needed for specific drivers to operate efficiently with certain video cards.
Be mindful of network connections. Clients can connect to the X server from the local host or from over the network. Configuration files such as X0.hosts control this access, along with the Xauthority file covered in the man page on Xsecurity. Remote machines also can connect to the desktop manager to gain access to resources not on their machines. This is controlled through the XDMCP protocol, which most desktop managers support.
When troubleshooting the desktop environment, make sure to take the simplest approach first. Determine whether the problem is with the user or the system. A simple approach is to create a test user account and see whether it experiences the same phenomenon. This is a great data point when it comes to troubleshooting the desktop.