Not sure if everyone can see my above reply (some problems posting), so I'll post it again:
It appears that the problem has been resolved, somehow.
I've downloaded a mod to see how it worked there, and I've noticed that Techtree.xml was read-only. So I've also checked read-only on my own Techtree.xml. I can't remember if it worked right of the bat, but when I unchecked it again and restarted the game, the game all of a sudden began reading the file from my Mods folder! After that I've made changes again, without making the file read-only and it worked again; and again, and again... It now works fine, just like Planetaryimprovement.xml.
Since that read-only box was the only thing I messed with, I must assume that it was responsible for the problem somehow.