X very slow and shutdown problems

I am running the latest xorg version and have setup x to run with xfce4. I am having trouble.

1.First of all, when I type startx, the screen blanks and flashes for a while and X takes a long time to start - possibly 2-3 minutes or more. It then takes additional time before the icons and panel appear.

2.If I attempt to start a program, there is around a 30 second to 1 minute gap between mouse click and the program starting.

3. On shutdown of X, at first the problem was a flashing screen as if the system was hung / frozen. I had to ctl-alt-delete and eventually the machine would reboot. Today, I have attempted to log out of xfce and the system just seems to have hung. I clicked logout 10 minutes ago. Obviously, this worries me that it may cause damage to my machine.

I am not sure where to start in identifying and fixing these problems. Please can somebody help me.
 
Code:
atop (it has keys, "M" etc)
pstree |less 
script -a why_slow.log startx # the log may show clues...
...
#if a program is not installed...
cd /usr/ports
make quicksearch key=atop
 
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