Firstly, can you type in Persian in the word-processor? To do that, click on Tools - Languages, tick the box "enable for CTL", and select Persian. If you can type Persian in Writer, then you have Persian support correctly enabled.
As for other applications, they may not support Persian. I don't think the Gnome terminal does — it didn't the last time I looked — but mlterm does.
http://sourceforge.net/projects/mlterm/
The standard version of vi doesn't work either, although there are versions of vim that do
http://vimdoc.sourceforge.net/htmldoc/arabic.html