Looking at decompiled source of the 1.11 server release, I found where it converts to lowercase: net/minecraft/server/MinecraftKey.class
It stores the name in a String (named "a", in this obfuscation) which is what's used to make the File reference. This occurs in the constructor, and it's here that it converts the text to lowercase.
I can confirm this, as well.
Looking at decompiled source of the 1.11 server release, I found where it converts to lowercase:
net/minecraft/server/MinecraftKey.class
It stores the name in a String (named "a", in this obfuscation) which is what's used to make the File reference.
This occurs in the constructor, and it's here that it converts the text to lowercase.