I don't think it's the font. I've just tried this MWE with several font
choices,
\documentclass{book}
\usepackage{polyglossia}
\setdefaultlanguage{sanskrit}
\setmainfont{Sanskrit 2003}
\begin{document}
ā ī ū ṛ ṝ ḷ ḹ ṭ ḍ ṅ ś ṣ ḥ
\end{document}
Sanskrit 2003 gives this:
[image: image.png]
Murty Sanskr̥it gives:
[image: image.png]
So there's definitely something wrong that isn't local to one font.
If we remove the \setdefaultlanguage{sanskrit} line, all is well.
That's as far as I've got just now.
Best,
Dominik
