Naturally when TNT is lit it falls South East (some sort of weird gravity?)
To fix this, place blocks around the unlit tnt so that it doesnt fall at an angle.
S = Stone (any block)
R = Redstone wire (projectile ignitor)
This will cause the TNT to fall straight down, taking the impact directly in the middle, causing it to shoot straight up.
Also, with the new way TNT works as a entity (lit tnt) you dont get extra push from those back 3 TNT. Previous MC releases the water pushes the lit TNT, now it doesnt.
You can fix this by adding a compression TNT to the back that pushes the "fuel" tnt forwards under the "projectile"
What I do:
Light the compression TNT a couple of ticks ahead of the fuel tnt. When the compression tnt goes off behind lit tnt, it pushes it forward. Shortly before the fuel tnt goes off, drop the projectile tnt (like you have it now).