Currently under the NBTList#remove method you're using

while((id = this.indexOf(o)) != -1) {
    this.remove(id);
}

While this can normally be fine this sucks when you're removing a string from a string list tag where duplicates are likely to be more apparent causing issues where the tag is just completely empty when you only wanted to removed one element.

I wouldn't call this a bug but should likely be treated as one when the javadocs explicitly state that it "Removes the first occurrence of the specified element from this list" (Copied form List interface)