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This is the file http://tinyurl.com/c5wtlco

Movie is in mp4 format.
I tried everything, subtitle workshop, notepad, wordpad, different combinations. In workshop they are displayed properly, I tried to replace each character with number 000x (0001, 0002...etc), and then replace them back. But, VLC won't display these characters properly č ć š đ ž. Instead I get question marks and I with " above letter. Depends on character. Encoding is proper in VLC 1250. Other subtitles work.

Edit: I tried another subtitle with movie and again I have question marks instead of characters.

Edit 2: Now I tried totally different subtitle that has nothing to do with movie, skipped to part where Serbian characters appear and I get question marks? Same title that works normally with belonging movie.

How can a movie affect subtitle in this case?

I copied both streams (video and audio) into mkv and I have no problems.

So VLC has problems with mp4 file and latin-cyrilic (Serbian) subtitles.

Edit: Now this is strange and it's a final check. Video had separate english subtitle in srt format. I deleted subtitle and suddenly Serbian subtitle started working properly.

With final examination, VLC has problems displaying Serbian subtitle while this English was active (Track 1)?

What font do you use?
Tools > Preferences > ( Show settings = Simple ) > Subtitles & OSD:
Default encoding [Eastern European (Windows-1250)]
Font [Arial] << choose a proper font which can handle serbian characters
The file you have provided should be O.K. with these settings.

As I said, on final statement, movie came with english subtitle (.srt) when I putted Serbian subtitle in same folder, charaters were displayed as question mark. But when I deleted english subtitle file, Serbian began to work normally.
And yes, every subtitle works normally Arial - 1250 encoding.

Like there was some conflict between subtitles and I do not know how could VLC can do that. I will try something more, and if that is the case, you can try both subtitles (same folder in a movie) on some other movie if you like.

Edit: I've tested it with another random movie. It seems that this http://tinyurl.com/d5p4gog subtitle is making other Serbian character based subtitles into question mark.
How is this possible?
This and above in first post subtitle are in same folder as movie.

Unicode autodetection. If one of subtitles is in unicode format, then another subtitles are treated the same way.
Solution: convert all subtitles to the same format (Notepad: File > Save as... > Encoding: ANSI or UTF-8).