Not sure of the exact cause, but the lights seem to be one of the first things to go on the factory units. I'm pretty sure you can fix it, but I don't think it's worth it since you can probably find a replacement stock deck for like $20-30.
Definitely NOT worth trying to fix. Mine werent working when i bought my 4runner. I recently replaced the head unit so I took the front off the old one to see if it was worth fixing. Its a bunch of surface mount chip LEDs. Since you mentioned they blink, that means its not the LEDs that are bad. All the LEDs are routed to large quad flat pack IC. I didnt look close enough to determine if its a microcontroller or an LED driver. If its a micro, your SOL, if its an LED driver you might be able to replace it, but unless you are experienced with electronics and have the correct SMT soldering/desoldering tools, its just not going to be worth your time...
Thanks! I'll try to find a cheap replacement and attempt to remove the old one and put in the new one. I assume it'll be the same wiring if I buy the same unit. (and hope that it fixes the issue).
Now, that i think about it, its likely not the IC either. Its likely a loose connection somewhere within the unit, The problem would be trying to that down. Why not replace it with something modern. Aftermarket units arent really all that expensive, unless you want it to be. I bought a double din unit with touch screen, bluetooth and all that jazz for $400.