Updating my post with more details and a screenshot:
Since the last minor version, I no longer see the boxes.. however, letters and their modifiers are not joining.
I have tested this with some other Indian languages and they all have the same display problem with their base letters and their modifiers appearing separately, without joining. They look fine in gedit but not in Sublime Text 2.0.1
For example, copy this Telugu word, తెలుగు in gedit and sublime to see the problem.
Or another language, Hindi हिंदी word.
Btw, I could not attach the 8 kb screenshot to this post (got an error), so please see it here:
The first example contains 3 base letters with each having one modifier, so they are displaying like 6 separate letters in ST, instead of 3 compund letters.
Fixing that single issue will support the languages of one billion people (or may be more) in Sublime Text editor.
And I am going to license every major version of it for the next 20 years! So, please...