Cycles Bake yeilding bizarre textures and wrong colors- any ideas? I've created a building for export and use in a game engine. Here's a picture of the building in the Materials Viewer of the Viewport.  This is what I'd like it to look like once I've successfully baked the textures.



I am baking the textures into a single image file by UV Unwrapping the model, creating a new texure, and placing the image texture in each material node. Picture is below (new image texture connected to final UV map is at the top of the node viewer):



After Diffuse Baking (I'm not needing shadows and I'll do the Normal map later), I'm left with this texture: 



I know it's hard to tell how bad this looks, so here's an idea of what this looks like once it's pasted on the exported object. By clicking on different faces, I can see in the UV Editor how many spots aren't rendering in the correct color (the green windows for example, largely come out tan on the baked texture.  Many faces of the red-roofed staircase on the end have a combination of red and tan textures on it).  



I am rather new to Blender, but I don't even know where to start with troubleshooting this.  What am I doing wrong? I would be glad to upload the .blend file if someone can provide instructions. Thanks!
You've probably moved on by now, but for anyone with the same question, I had a similar issue just yesterday. I never quite figured out why exactly it was happening, but I eventually got the problem to go away by cleaning up my mesh. This included

adding and connecting some vertices to break up some large planes getting stretched at weird angles
dissolving unnecessary edges and vertices
deleting entire planes that were not going to be visible in the render
separating a part that I had awkwardly extruded and probably had some weird relationships with other vertices.