Z-ordering & shaders in Klepto's mod

Firstly, I'm pretty new to MiniB3d so I apologise if I'm missing something glaringly obvious but anyhow, I'm trying to create a basic material system using klepto's version of MiniB3d but I'm having issues with the z-ordering on alpha masked textures.

Currently if I load a texture with the Alpha flag, the textures are drawn over each other and I can't seem to sort the problem out.

I attempted to use a simple GLSL shader, which works fine if I use the discard function, but I cannot use the alpha channel for transparency. It works if I load the texture with the alpha flag, but again the ordering gets messed up.

This is my current code, adapted from the shader example:

Local Decal:TTexture = LoadTexture("Texture.tga")
tex.BrushTexture(Decal,0)

BrushShaderTexture(Tex,Decal , 0)

InitShader(Tex)
AddShaderObject(Tex,"media/new.vert","media/new.frag")
Tex.ProgramAttriBegin()
	Tex.SetUI1("texture" , 0) 
Tex.ProgramAttriEnd()

PaintEntity(mesh, Tex)
ActivateShader(mesh, True)

This is my vert shader:

void main()
{
	gl_Position = ftransform();
	gl_TexCoord[0] = gl_MultiTexCoord0;
}

this is my frag shader:

uniform sampler2D texture;

void main()
{
	vec4 texColor = texture2D(texture, gl_TexCoord[0].st);
	gl_FragColor = texColor;
}

Anyone have any suggestions? Thanks!