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Help Green light of death....

Okay, conspiracy theory here....

Either the phone is broken.

Or, it is a rooted phone somehow, in order to have enabled the coloured trackball notifications (which I have but only through rooting).

So question for the OP - does the phone as a whole work okay? And, on boot at the solid X symbol on the phone, do you see and unlocked padlock symbol at the bottom?
 
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Maybe a little green man from the declassified planet Pluto has crash landed in your backyard and his only safe haven was a tiny little white ball - that made him feel safe because it closely resembled his crashed spaceship - which just so happened to be attached to a device known as the Nexus One and he's currently working on the electronics of the device to reconfigure it to fly him back home. Whenever you see the green flash it's the little green man glowing with delight because he's oh-so-much closer to finalizing the phones new programmed flight scheme.
 
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Rusty stated..
You have to root to get the other colours, although I hear an incoming call when using a Bluetooth headset causes a blue light.

I've just been RTFM'ing & on P 24 it states ...
Trackball state Meaning
Flashing white Incoming call.
Flashing blue Incoming call when connected to a Bluetooth headset.
White pulse Notification received. You can configure the trackball to pulse once or repeatedly when you receive a new notification. See
 
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I had this strange issue myself till i uninstalled cyans rom.
Full color trackball notifications is the feature of Cyanogenmod V5.0.4.1 ROM.

This is how it works:
- Screen on: incoming whatever - one white flash
- Screen off: notification - one white flash, then colored flash
- SMS, Gmail - green flash
- Missed call, twidroid - cyan flash
- Incoming call - rapid white flashing
- Incoming call while on bluetooth - rapid blue flashing
 
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