I noticed that you're not using most up to date BS.Player version.
Therefore...
maybe first try an updated language file: http://peterg.coi.co.il/תרגום-BSPlayer.htm (
http://forum.bsplayer.com/40907-post7.html ).
Only if that doesn't help read on... This maybe related to a known bug in the last three builds. As a temporary solution: Under (rightclick >) Options > Preferences > Subtitles [Subtitle properties] ... (1) ... verify setting of the box "Use new subtitle parser/renderer"; try if (de)selection makes any difference. (2) ... verify what script is selected under [Font]; if (e.g.) Western .. change it to correct script. Another possibility is to load the file Hebrew.lng (in subfolder "lang" of BS.Player's installation folder) in Notepad. Without making any changes click on "File" > "Save as" and verify at the bottom what Encoding is selected (e.g. UTF-8 or ANSI). Now change this setting and save file. (Please let us know the result!)