Bounding Spheres When They Choose To Be

After much reformatting and deleting of my code, I significantly downsized my engine. You would think that this would make things simpler (which was certainly my intention) but alas, I still feel like I am stuck in the mires of a swamp. I can now display wire mesh bounding spheres around solid cubes. These spheres transform accurately with their inner objects, and upon collision, they correctly change color. However, two problems still remain which I am currently working on resolving:


1. When the bounding spheres change color (I do this by passing the shader a different light color when the spheres are colliding), the inner objects visually change color as well. I say "visually" because when I debugged the code, I noticed that the objects actual colors had not touched, but were displaying as the overriding bounding color. These two objects should be entirely separate in that respect but somehow, they are linked where one is overshadowing the other-- I need to figure out what the link is here.

Here is what the cube (untextured) in a bounding sphere looks like:

2. Another issue that arose is that the bounding spheres do not show up around other forms, like the cylinder. Instead, scaling of the form's bounding volume results in scaling of the cylinder, which is clearly not what I want. Again, there is an unwanted link in here somewhere and I am working now on determining where and what it is. I have a feeling that I will need to reformat the code yet again. One idea that I have though is that perhaps I am passing in a modified matrix that should have been set to an identity somewhere, and this is causing incremental changes. I just don't understand why this is affecting everything but the cubes though-- what makes them different?

Here is what I see when I apply the bounding sphere to a cylinder model (untextured):

These are the two main issues that I am facing right now. I have made good progress but want to iron this out before I can comfortably move on. This is what I will be working on tonight.