I brought an illustrator file into After Effects (latest version).
I converted the .ai file through "create shapes from vector layer" in the After Effects timeline. Once I do that, as you see the from the screen shot, the first half of the logo is fine. But the Energy Programs part only shows the outline of the two words: Energy Programs. In my .ai file, thse have a fill.
How can I add a fill to each letter shape in After Effects?
You will likely have to drill into the actual shape layer groups and reorganize them suitably. What you see pretty much indicates that you used a stroke type that isn't compatible with AE and could not be converted automatically. That being the case, I would strongly urge you to actually read the online help on what features are supported and how to best prepare your AI artwork to avoid such problems.