My bet is that you're not using multitexturing with shaders correctly but it's hard to tell.  Besides binding the two textures to different units, you need to set the uniform's in the shader to the correct units.  So if you bind your color texture to unit 0, you call glUniformi("colorTexNam", 0) to tell the shader to grab color information from the texture at 0.  You don't tell the shader the id of the texture, which can be a little confusing.

This is a guess because I don't know everything you're doing (once again, try to create a standalone Java app to experiment).