In the preferences of the latest VLC 1.0.1, in the "Subtitles & OSD" section the greek subtitle encoding is "Greek (Windows-1256)" instead of "Greek (Windows-1253)" as it was in VLC 0.9.*
Windows-1256 is an arabic encoding:
http://en.wikipedia.org/wiki/Windows-1253
http://en.wikipedia.org/wiki/Windows-1256
And "Greek (ISO 8859-7)" is not a suitable replacement for "Greek (Windows-1253)", there are differences with the position of Ά.
This is a serious bug and regression of VLC 1.0.* over previous versions of VLC.