When you apply the brakes the brake lights won't work, but the turn signal indicators in the truck will light up.
Someone will correct me if I'm wrong but I believe the brake light is the directional light and vice-versa. The same filament within the dual filament lamp is used to indicate braking or turning.
There are only 4 wires that serve the rear lighting:
1. Brown wire - supplies parking (one of the filaments in the dual lamp), marker and license plate lights. Energized through the headlight switch by pulling at least halfway out. These lights stay on at all times that the H/L switch is in the parking light position (or headlights).
2. Light Green wire - supplies power to the reversing/back up lamps. It is energized when the gear selector is in "R" and the back up contacts within the neutral safety switch close.
3 & 4. Dark Green & Yellow wires - these wires supply the combination brake light/directional lights which are the other filaments within the dual filament lamp. Dk Grn is for the RH side and Y is for the LH side. The power can come from either the brake switch or the directional switch. It gets involved because the splitting of the signal happens in the MFS (multi function switch).
So, long story short - by design, stepping on the brake should illuminate the directional filament (because it is also the brake filament.
If you have a turn signal on and then step on the brakes - the side that is indicating the direction of your turn will act as a blinker. The other non-turn side will go to a steady light and act as a brake light.
Having said all that - I have to ask what exactly you mean by this:
When you apply the brakes the brake lights won't work, but the turn signal indicators in the truck will light up.
#1 - Do you mean that you never - at any time - get any lights at all when you step on the brakes?
#2 - Or do you mean that when you press the brakes the brake lights don't light up but the directionals do?
If you mean problem # 1- begin by checking the brake light switch
If however, you mean #2, did the explanation above clear things up. Or did I only confuse the issue even more?
If the brake light switch is in place (and switching the power to the white wire off and on as designed), you have a problem in the brake/blinker common area of the MFS.
Since you are having a big problem just even changing the position of the MFS stalk - I would not be surprised if the brake light switch proves good and the MFS is found to be shorted.