The filename is not the metadata TITLE - they may look similar but they are definitely different things.
What should happen is that the files list (usually to the right of the tag panel) which shows the files and a number of the tag fields in a table should also show the data that you see in the tag panel (if you select a single file).
Then: the windows explorer is not the best test bed to check tags in flac files. there are some threads in this forum that report that the explorer refuses to show tag fields once one exceeds a certain length. So I would stick to MP3tag and see if the tag fields are filled.
(see e.g. here:
What you could also check: do you only have FLAC tags in your files or also ID3 tags?
The easiest check is to select a single file and then press ATL-T to open the extended tags dialogue. The window title of that dialogue shows the name of the tags. Ideally, it should only show FLAC for flac files. Any ID3V2.3 or so indicates that something has not tagged the files properly.
So, what do you expect to happen after you have pressed Ctrl-S to save the tags? That the filename changes?