I tried to use the options SMPlayer passes to MPlayer on the command line. I had to remove the -slave and -wid options in order to make the file play. However, I don't get to see the subtitles, cannot make them visible, and cannot switch between different subtitles. If I remove the -osdlevel 0 option the subtitles are visible and choosable, but they will appear on the video, not on the black borders. I don't think that the black borders are even added and without them I cannot see whether the problem is reproduceable on the command line.
C:/Program Files/smplayer-portable/mplayer/mplayer.exe -noquiet -nofs -nomouseinput -sub-fuzziness 1 -identify -slave -vo directx, -ao dsound -nokeepaspect -priority abovenormal -framedrop -nodr -double -wid 459206 -colorkey 0x020202 -monitorpixelaspect 1 -ass -embeddedfonts -ass-line-spacing 0 -ass-font-scale 1 -ass-force-style PlayResX=512,PlayResY=320,Name=Default,Fontname=Arial,Fontsize=18,PrimaryColour=&H00ffffff,BackColour=&H00000000,OutlineColour=&H00000000,Bold=0,Italic=0,Alignment=2,BorderStyle=1,Outline=1,Shadow=2,MarginL=20,MarginR=20,MarginV=8 -fontconfig -font Arial -subfont-autoscale 0 -subfont-osd-scale 18 -subfont-text-scale 18 -subcp ISO-8859-1 -vid 0 -aid 0 -subpos 100 -volume 100 -nocache -ss 1353 -osdlevel 0 -vf-add screenshot -slices -channels 2 -af scaletempo,equalizer=0:0:0:0:0:0:0:0:0:0 -softvol -softvol-max 110 -nofontconfig [path/]filename