Currently Most of the Malayalam fonts in Wikimedia server are based on unicode 5.0. It cause display clutters in Server rendered pages. As far as now, only unicode 6.0 compatible font available for Wikimedia sites' server side is Anjali, which has a buggy Linux implementation. Please update Malayalam fonts to unicode 6.0 compatible. Unicode moved from 5.0 since April 2008, so I hope it is okay to use even hacked fonts, if there are no "upstream fonts" available.