I think I do recall reading something about holding the power window switches up for a few seconds to regain control from the switches (might've only been for the drivers power window switches) for a Prado, but I'd imagine they'd work similarly. If Stef's suggestion doesn't work, you could have a look at this. I don't know how helpful this will be but it's better than nothing and might give you a few other things to have a look at before going to an auto leco. Might find something obvious, you never know
These drawings might help a bit if you can read schematics and if the drawings suit an 06 model Hilux:
http://www.scribd.com/doc/84897170/Toyota-hilux-wiring-diagramPage 151 shows a simplified drawing and sheet 16 (page 234) in Section M shows a more detailed schematic, and Section G (page 41) shows locations and electrical cable routes.
It looks like it's powered from the 30A power fuse (which you said all fuses are ok), runs to connector J16(A) and J17(B) which are located behind the glove box near the relay/fuse panel there (from page 41), then runs to connector J26(A) and J27(B) which are located on the drivers side around foot level near the accelerator pedal (from page 41), and also runs to connector J13(A) and J14(B) which are located in the same position as the latter mentioned connectors but on the passenger side (from page 41), and then runs to all the window switches. And it looks to be grounded in the J28 connector located on the drivers side just above foot level (from page 41) which looks like a plug that's plugged in to a metal bracket that's screwed to the body.
Something might've come loose. I don't think it would be the ground because numerous other circuits use the same ground and you said everything else works fine. So chances are it could be a connector or cable if you were cutting near them but they are all in the cab so unless a conductor was corroded or fatigued and the vibration was enough to break it off I don't see the problem being in there.
What I would probably do if you can, is pull out the IG1 relay located in the relay block behind the glove box (from page 38) and see if there is a drawing on the side of it telling you which pins are the coil and which are the contacts. If there is no drawing, grab a multimeter if you have one, put it on ohms and test between pairs of pins until you find the coil connections (I'm thinking you could measure about 60 ohms across the coil unless the coil is open circuit). Once you have found the coil connections, grab a couple of bits of wire and connect the relay coil to the battery and see if you can hear (or feel) it clicking to see if it's working properly.
I'm not entirely sure what the relay is like and what the plugs look like since the only electrical work I've done on my 2013 lux is installing some led reverse lights (speaking of which I need to look in to filtering the noise out that the led lights cause on the stereo when the lights are on) and preparing for fitting an led bar when I man up and spend the money
But hopefully this might help a little bit
Good luck!