Manual:$wgFixMalayalamUnicode

Details
Set this to true to replace ZWJ-based chillu sequences in Malayalam text with their Unicode 5.1 equivalents. This only works if $wgLanguageCode is set to "ml". Note that some clients (even new clients as of 2010) do not support these characters.

If you enable this on an existing wiki, run maintenance/cleanupTitles.php to fix any ZWJ sequences in existing page titles.