Games no Longer Responsive to Controller

[The Current Mood]

My controller (a USB Xbox 360) won't work anymore when running my games, while they work perfectly fine otherwise they won't recognise any input I make.

When I run PCSX2 via the 'Boot CDVD (full)' and are taken to the 'main menu' for the PS2 the controller works fine and I can navigate the menu successfully.
Only when I launch the games via 'Boot CDVD (short)' are they unresponsive.   

I have no idea what could have caused this as yesterday when I playing them there was no issue and only today when I launched them did the issue occur. 
To the best of my admittedly limited tech ability, I tried to fix the issue but cannot so any advice would be appreciated even if it ultimately doesn't work.

Thanks in advance for any help you offer.
If there is any missing information that would help identify the problem please let me know.  

[The Current Mood]

Firther Information that may help:

-the games are 'Scooby-Doo! Night of 100 Frights' & 'Scooby-Doo! Mystery Mayhem'

-version of PCSX2 is 1.4.0

-screenshots of the settings currently applied to Lillypad are included

[vsub]

Just for a test(don't click Ok\Apply after that)
Go to Pad1,click on "Clear All" and try setting any button.
If the in Device column it is not saying the same thing as before(before clicking clear all),then you have the usual problem with xinput gamepads and windows

If that's the problem,you have to reconfigure the gamepad up to 4 times(every time it stops working)

[The Current Mood]

Just for a test(don't click Ok\Apply after that)
Go to Pad1,click on "Clear All" and try setting any button.
If the in Device column it is not saying the same thing as before(before clicking clear all),then you have the usual problem with xinput gamepads and windows

If that's the problem,you have to reconfigure the gamepad up to 4 times(every time it stops working)

That's fixed the issue.

Apparently all the controls were registered with 'Input Pad 0' rather than 'Input Pad 1'.
Strange why it would suddenly change it like that, it's working now so it doesn't really matter. 

Thanks for the help.

[vsub]

That's windows thing....it sets XInput devices to a number based on which one was started first
My gamepad can work in wired and wireless mode
If I connect the dongle and restart window,then wireless mode will be set to XInput0 and even if I disconnect the dongle and connect the gamepad with the USB cable,the wired mode will still be registered as XInput1
If I do the opposite after the windows restart,wired will be XInput0 and wireless XInput1

Also if you connect the dongle\usb after they are already registered to some other USB port,then they will be registered as XInput2 and XInput3
There are 4 XInputs so if you configure them all,then pcsx2 will always work no matter what number windows decides to put on the gamepad

Some PC games support only inputs from XInput0 which can be annoying to fix and that fix will be temporary.