I'm guessing you are using Windows Vista?
The problems seem similar to what I had, so I'm guessing you need to look into the way Vista uses permissions for certain files. It took me some time trawling through the different file options and permission settings.
In my case I was logged on as an administartor, had done the neccessary installations, everything appeared fine. Even looking in the techtree files as Achilles suggests, shedded no light, as all files were present and correct. But when running the game, it somehow appeared to still be using the stock techtrees.
Basically what I found was that windows had let me make the neccessary changes and instal the new files. However, because I did not have the appropriate permissions ticked under the windows file options, it ignored the changes I had made and continued using the original files.
It really confused me for some time. Why windows didn't just tell me at the beggining that the permissions were wrong is beyond me. Vista is a strange system at times.
Having said all that, if you are not using Vista, chances are you have done something wrong yourself. Start again from scratch with a fresh instal of the game and patch.
Does that make sense? Sorry I've been up working all night.
