I have sort of a similar Problem.
My Soldiers do not get any Medals for Mission Completition, Base Defense, Base Attack, Terror.
Working Medals:
Crimson Heart (serious wound)
Military Cross (5 aliens/single mission)
Order of Gallantry/Merit/Terra (5, 10, 20 alien kills)
Not working:
Service Medals (10, 20, 30 Missions)
Citation of Valor (Base Attack)
Citation of Courage (Terror)
Citation of Bravery (Base Defense)
I just recently installed the XCE Mod and added some tweaks for my playing:
buildings.xml
weapons.xml
Soldierimagesfemale (folder)
soldiernamesfemale.xml
weapons_gc.xml
armours_gc.xml
gameconfig.xml (ufo/terror landing duration)
loadouts.xml
So nothing that interferes with medals i think.
Vanilla works fine.