If I had to guess it is material mapping.
Usually multi material objs use materials with "usemtl" you had better then use the correct textures defined in the accompanying mtl file.
For example here is a simple cube.obj:
# Blender v2.77 (sub 0) OBJ File: ''
# www.blender.org
mtllib cube.mtl
o Cube
v 1.000000 -1.000000 -1.000000
v 1.000000 -1.000000 1.000000
v -1.000000 -1.000000 1.000000
v -1.000000 -1.000000 -1.000000
v 1.000000 1.000000 -0.999999
v 0.999999 1.000000 1.000001
v -1.000000 1.000000 1.000000
v -1.000000 1.000000 -1.000000
vn 0.000000 -1.000000 0.000000
vn 0.000000 1.000000 0.000000
vn 0.000000 -0.000000 1.000000
vn 0.000000 0.000000 -1.000000
vn 1.000000 -0.000000 0.000000
vn -1.000000 -0.000000 -0.000000
usemtl Red
s off
f 2//1 4//1 1//1
f 8//2 6//2 5//2
f 6//3 3//3 2//3
f 1//4 8//4 5//4
f 2//1 3//1 4//1
f 8//2 7//2 6//2
f 6//3 7//3 3//3
f 1//4 4//4 8//4
usemtl Blue
f 5//5 2//5 1//5
f 3//6 8//6 4//6
f 5//5 6//5 2//5
f 3//6 7//6 8//6
Here is its mtl:
# Blender MTL File: 'None'
# Material Count: 2
newmtl Blue
Ns 96.078431
Ka 1.000000 1.000000 1.000000
Kd 0.000000 0.004612 0.640000
Ks 0.500000 0.500000 0.500000
Ke 0.000000 0.000000 0.000000
Ni 1.000000
d 1.000000
illum 2
map_Kd blue.tga
newmtl Red
Ns 96.078431
Ka 1.000000 1.000000 1.000000
Kd 0.640000 0.000000 0.000630
Ks 0.500000 0.500000 0.500000
Ke 0.000000 0.000000 0.000000
Ni 1.000000
d 1.000000
illum 2
map_Kd red.tga
So load the appropriate material and texture, don't bind materials in the order the editor assigned them and do not use the order from the file (as you can see obj references Red, Blue; but the material file lists Blue Red)