The order depends on where exactly you put your cursor when you click and hold on the files as you drag them. Whatever file the cursor is actually over when you drag the list of files will be the file that appears at the top of the list. So to avoid this, always put the cursor over the first file in the list then click and drag.

Yes this is stupid but that's how it works.

Sometimes you can drag and drop the folder (as opposed to the files) onto flac frontend and the files will appear in the right order. Other times this doesn't work at all. I haven't figured out why yet.