I have installed Ubuntu 16.04 and there is a bug related to my mouse (RAT 3). I cannot use the left click properly. Sometimes I have to open a Window in order to use the mouse in another window.
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We need more information. How is the mouse connected, have you tried plugging into another port. What else have you tried - have you done any research on this? – Tim Apr 23 '16 at 21:19
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Try http://askubuntu.com/questions/92546/cyborg-r-a-t-3-gaming-mouse-stops-working-after-a-while-and-or-misbehaves and http://askubuntu.com/questions/331388/madcatz-rat-3-mouse-issues and https://wiki.archlinux.org/index.php/Mad_Catz_Mouse – Tim Apr 23 '16 at 21:21
2 Answers
This is a common Ubuntu bug. Try to do this: Back up the xorg.conf file
sudo cp /etc/X11/xorg.conf /etc/X11/xorg.conf.orig
May the files doesn't exist. This is not necessary.
Anyway edit the file with sudo nano /etc/X11/xorg.conf
and paste this:
Section "InputClass"
Identifier "Mouse Remap"
MatchProduct "Saitek Cyborg R.A.T.3 Mouse"
MatchDevicePath "/dev/input/event*"
Option "ButtonMapping" "1 2 3 4 5 6 7 0 0 0 0 0 0 0"
EndSection
Press Ctrl+O to save and Ctrl+X to exit the editor. Reboot for functionality!

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This article from the Arch Linux wiki worked well on my laptop with Ubuntu 16.04.
Here are the most relevant parts:
The Disable Button Solution
The issues are caused by an interaction between R.A.T Mode button and the X Server. To restore proper function, the 'Mode' button must be disabled, as follows:
With root privileges, create and edit the file
/etc/X11/xorg.conf.d/50-vmmouse.conf
Add the following content :
Section "InputDevice" Identifier "Mouse0" Driver "evdev" Option "Name" "Saitek Cyborg R.A.T.3 Mouse" Option "Vendor" "06a3" Option "Product" "0ccc" Option "Protocol" "auto" Option "Device" "/dev/input/event4" Option "Emulate3Buttons" "no" Option "Buttons" "7" Option "ZAxisMapping" "4 5" Option "ButtonMapping" "1 2 3 4 5 6 7 0 0 0 0 0 0 0" Option "Resolution" "3200" EndSection
After restarting your X server, the mouse should be fully functional, including the two lateral buttons.
[...]
Manual Button Mapping Fix
Please note that there are two different versions of the R.A.T.3 mouse which are Saitek and Madcatz, this must be input correctly into the "MatchProduct" or you will run into the same issues.
First find out the ID and the Name of the mouse :
xinput list | grep "id"
In you should see your mouse labeled as "Madcatz Mad Catz R.A.T.3 Mouse" or "Saitek Cyborg R.A.T.3 Mouse". Note the device id number and then input the following command :
xinput query-state ID
(Where ID corresponds to the ID number of your mouse)
Note which 'mode' color is currently active (red/blue/purple) and which button numbers correspond to the current 'mode' by being either "up" or "down". Change the mouse 'mode' and and retype the above command, noting which buttons change state to match the 'mode'.
Example:
U = up D = down U U U U U D D U U D D D U U Option "ButtonMapping" "1 2 3 4 5 0 0 8 9 0 0 0 13 14"
Where buttons 10, 11, and 12 have been identified as 'mode' buttons, so they can be disabled by with zeros.
When you have identified which button numbers correspond to the mouse 'Modes', you should be able to edit your xorg.conf file and disable them by inserting a zero in the appropriate point in the button sequence. Open one of these files in your chosen editor:
/etc/X11/xorg.conf /etc/X11/xorg.conf.d/50-vmmouse.conf
Create a block that overwrites the mode buttons as follows:
MadCatz R.A.T.3:
# RAT3 mouse Section "InputClass" Identifier "Mouse Remap" MatchProduct "Madcatz Mad Catz R.A.T.3 Mouse" MatchDevicePath "/dev/input/event*" Option "ButtonMapping" "1 2 3 4 5 6 7 8 9 0 0 0 13 14 15 16 17 18" EndSection
This configuration worked for me on my old Saitek Cyborg R.A.T.3:
# RAT3 mouse Section "InputClass" Identifier "Mouse Remap" MatchProduct "Saitek Cyborg R.A.T.3 Mouse" MatchDevicePath "/dev/input/event*" Option "ButtonMapping" "1 2 3 4 5 0 0 8 9 0 0 0 13 14" EndSection