As a workaround, try unplugging your mouse and plugging it back in. I run into this issue when the mouse is plugged into my laptop when Ubuntu boots up. Using this workaround fixes the issue for me.

The reason (as I understand) that this particular mouse misbehaves on Linux is because of the mode button. In terms of key presses, each mode corresponds to a different button being held down. For my mouse (R.A.T.7) the mode buttons are 13, 14, and 15 for red, blue, and purple respectively.

I don't know if yours are going to be the same, but there's a nice and easy way to figure it out. Open a terminal and type:

xinput list | grep "id"

Find the entry that has the corresponding label (for me it's "Saitek Cyborg R.A.T.7 Mouse") and note the ID to the right. Then, type:

xinput query-state ID

(Where ID corresponds to the ID of your mouse)

Note which mode color is currently active, switch it to the next one, and retype the above command. Do that one more time.

Now that you know which buttons correspond to the modes, you should be able to edit your xorg.conf file appropriately. Type:

gksu gedit /etc/X11/xorg.conf

(Obviously you can use a different text editor if you feel more comfortable with one. If you use a command-line text editor, use sudo instead of gksu.)

You'll want to insert a block that's similar to this:

Section "InputClass"
    Identifier      "Mouse Remap"
    MatchProduct    "Saitek Cyborg R.A.T.7 Mouse"
    MatchDevicePath "/dev/input/event*"
    Option      "ButtonMapping" "1 2 3 4 5 6 7 8 9 10 11 12 0 0 0"
EndSection

The important thing is the "ButtonMapping" part. Just go through the list of buttons sequentially until you get to the buttons that correspond to the modes and enter 0s instead.

You'll have to restart your X server for the changes to work, but this should fix it up!