Are the ini files not set to read only? Are you accessing the ini files in your Documents\Alpha Protocol\APGame\Config folder? What program are you using to edit them.
Also wanted to thank all of the posters here, especially MartinDee, for making an already great game freaking fantastic to play through. Runs, looks and controls like a dream now. You guys are awesome.
The only thing I didn't completely get was accessing the Unreal model packages. I had hoped to edit Thorton's face to something more sinister for my rogue playthrough, but every time I try to open umodel, it immediately closes. That aside, I didn't see anything verifying that that was actually a viable method of accessing the textures so I might be barking up the wrong tree for that anyway.