So I attempted installing this on my current mod setup with forge 489 and BC 3.3 and for some reason some NEI icons are transparent as shown in this image. The Rest of the mod works fine but this is very annoying and I wanted to know if there was any way to fix it.

I don't think this is because of additional pipes. There might be a render bug with another mod.
Have you tested with only AP and buildcraft?

I will try that when I get back from work