Well, I got a development release, I found the glyph of ല്ല looks resolved in FreeSerif, but positioned incorrect in FreeSans, then യ്യ looks normal in FreeSans and FreeSerif.

ണ്ണ, പ്പ, പ്ല, ല്ല, ന്റ, ര്ഗ, ര്ജ.

I have copied seven combinations from last comment for test. In the 20150829 build, they looks proper in both FreeSerif and FreeSans when I tested in Firefox; but when I copied them in BabelPad and LibreOffice, they still looks incorrect in FreeSans. BTW I found Unicode introduced a new character in Malayalam block, which encoded in U+0D5F.

Well, I got a development release, I found the glyph of ല്ല looks resolved in FreeSerif, but positioned incorrect in FreeSans, then യ്യ looks normal in FreeSans and FreeSerif.

ണ്ണ, പ്പ, പ്ല, ല്ല, ന്റ, ര്ഗ, ര്ജ.

I have copied seven combinations from last comment for test. In the 20150829 build, they looks proper in both FreeSerif and FreeSans when I tested in Firefox; but when I copied them in BabelPad and LibreOffice, they still looks incorrect in FreeSans. BTW I found Unicode introduced a new character in Malayalam block, which encoded in U+0D5F.