Have you tried using VirtualDUB and its subtitler plugin for applying subtitles to existing video files? Both are freeware.
The VirtualDUB subtitle filter will acccept SSA subtitle scripts, which are another export option in Subtitle Workshop. It appears in Subtitle Workshops export dialog as SubStation Alpha.
http://virtualdub.org
http://www.virtualdub.org/downloads/subtitler-2_4.zip
One everything is installed (VirtualDUB to its folder and Subtitler.vdf to Virtual Dub's Plugins folder) you're ready to go.
Export your video file from whatever editor you're using then load it into VirtualDUB.
In the 'Video/Filters' menu select 'Add' then 'Load'. Now browse to the 'VirtualDub/Plugins' folder and load in 'Subtitler.vdf'. Select it from the filters list and click OK.
A new dialog will come up asking you to browse to the SSA subtitle file you exported from either SubStation Alpha or Subtitle Workshop. OK your way out to the main VirtualDUB screen.
Now you have the option of previewing or exporting. When the video is exported the subtitle will be keyed to the video and saved as a new file.
When using this technique I do NOT apply subtitles to DivX or XviD!! Quality WILL suffer. DV works well enough as do MJpeg, HuffYUV, uncompressed etc. Once the subtitle is applied you can render it to DVD MPEG.