I've got 2 monitors connected to my laptop.

One is connected via HDMI and one is connected via USB displaylink.

When I boot up my computer linux thinks my DL monitor is on, but the screen is black (DL is not initialized properly for some reason).

The mate-display-properties fix
Its easy to fix using mate's display properties widget. (similar to gnome-display-properties)

Turn off DL monitor
I select the DL monitor, click off, apply

Turn on DL monitor
Then I select the monitor, click on, move it to where I want it, click apply.

Perfect!
Now lets try it with the command line after a fresh reboot.

Turn off DL monitor with command line
xrandr --output DVI-0 --off

Perfect. Now lets turn it back on...

Turn on using xrandr --mode (fails)
xrandr --output DVI-0 --mode 1920x1080
My system gets completely messed up and I have to reboot.
The DL monitor seems to mirror my LVDS monitor. I can move the mouse around but can't click on anything or make windows get focus.

Turn on using xrandr --auto (fails)
xrandr --output DVI-0 --auto
My system gets completely messed up and I have to reboot.
The DL monitor turns on but the graphics go all corrupt, black mixed with the picture, wherever I move the mouse redraws that part of the screen. It seems to have its own space rather than mirroring.
Its weird.

Solution?
If mate-display-properties could produce a commandline output or log for me to see what its doing I could just use the same commands?

verbose xrandr output (both screens positioned and working properly)
http://codepad.org/jJccaANW

You say:
and then you are passing commands to DVI, don't it should be HDMI ?
as your xranr info shows:
Try to run mate-display-properties from a terminal, you might get some output there when setting up the monitors.

Regards

Okay I tried running mate-display-properties from a console window inside the mate session and then turning monitors on and off with mate-display-properties.
I got a segmentation fault every time. and mate-display-properties ended. I tried running it in the foreground and background (without ampersand and with).
Besides the segmentation fault message, nothing else is shown.

[0] % mate-display-properties&
[1] 6209

[0] %
[1] + 6209 segmentation fault mate-display-properties

===================

Regarding HDMI vs DVI.

HDMI is the native HDMI graphics output on my laptop. When I boot up that works properly.

The DVI-0 is the Displaylink adapter. When I boot up the Displaylink monitor is on, but its black. It needs to be turned off and on again with mate-display-properties to get it to function normally.

This is what my setup looks like in mate-display-properties
http://i.imgur.com/gdZTQbI.jpg

Do you have a xorg.conf file in /etc/X11 ?(if you do please post it) If not it could be a good thing to have it there with all monitor settings you need, so then there is no need to set it up everytime the machine is turned on.

Regards