As you can see in the discussion at http://www.khmeros.info/drupal/?q=en/node/743#comment-1467, using letter-spacing (or text-align: justify) in CSS will break Khmer rendering. I have observed there is the use of letter-spacing in /theme/standard/styles_fonts.css. Other themes might use this CSS option as well.
I am not sure about the benefits behind this CSS option, but I suggest not to use it if it is just for the nice-looking purpose.
I have included some screenshots:
The more value the letter-spacing is, the more it breaks Khmer rendering.
After commenting out the letter-spacing, I got this fine rendering.
Related issue: http://moodle.org/mod/forum/discuss.php?d=68330#p327016
Soben