Ok, so heres the rundown... if your leds turn on and off... you might have a different problem. Next time the window doesnt operate properly, check if those leds are on. If not, then chances are its your switch and its only making intermittant contact, aka, its on its way out. If the LEDs are on, then either you have a differnet issue or you do have 2 different paths for the flow to run, the wiring diagram only showed one.
Now for "repair".. (keep in mind this is assuming the switch is the issue causing the malfunction)
If you want to keep a lockout switch functional, you have two options. Get a new switch box unit or wire your own switch in.
In the haynes manual, on page 12-28 (I belive it was) there is the wiring diagram incase you want to reference it. But there are at least two possible wiring color schemes. Apparently in all models, the 12V supply voltage is provided via a violet wire. The output of the lockout switch is either a violet or white wire. (if you have two violet wires then those are the two to use, if there is only one violet wire, chances are the other wire to use is the white wire, but no guarentees, this is the conclusion I came to so I think its right) But you will have to run a jumper between these two wires. DO NOT cut the wires as if you cut the 12V source wire you will not have any power at all, and therefore windows will be useless.. Either splice a wire between these yourself by stripping it and going from there, or go to walmart or somewhere that sells some electrical stuff. They may sell clips that splice a wire into other wires (One portion closes over the source wire, while the 2nd wire is closed into another area bridging the connections, sorry for the poor description here, I will try and get a name of the part later). Anyway, you have to wire a jumper between these two wires (the source wire and the output of the lockout switch). If you do that your windows should function properly if this was your problem. If you want, you can include an aftermarket switch in series with this wire to act as the window lockout. Where you locate this switch is up to you though.
I know my buddy has this issue, and I may be heading to his place this afternoon. I will offer to help him with this in order to get photos of the process if he wants to do it.