Dear Jan,
I am not sure this is what you are after, but I am aware of the following problems. I am not sure the Devanagari renderings I see on my screen will be duplicated in this email, but I try to give illustrations. All of these are on a Windows platform.
1. Some fonts that compose ligatures with a virāma incorrectly position a short i attached to the conjunct. Thus, e.g., the conjunct dmi has a "proper ligature" form in the font Arial Unicode MS and short i is attached correctly before it,
द्मि
. The same conjunct does not have a precomposed glyph in the font Mangal but uses a d with virāma, followed by mi,
द्मि
. The expected form would be to have the dependent i before the d with virāma. Interestingly, Arial Unicode MS renders correctly even when a ligature involves a virāma, so dghri in that font has the i before the whole thing,
द्घ्रि , whereas Mangal of course puts the i after the d+virāma,
द्घ्रि
. The positioning of superscript repha is also off in some fonts when a conjunct with virāma is involved; thus, Mangal presents rddhi as
र्द्धि (repha on d with virāma, followed by dhi). Interestingly (I've just noticed this while testing combinations), there is a partial problem in Arial Unicode too. If I compose rdghri, then (at least in MS Word) it appears with two rephas: one on द् and another on घ्र (with the short i positioned correctly to the left of the whole).
2. Certain (most? all?) Adobe products fail completely at rendering Devanagari ligatures. I am aware of this occurring (perhaps not in identical ways) in InDesign and Photoshop. Conjuncts get split into consonant+virāma combinations; thus, e.g. dghra renders as
द् घ् र (without the spaces). Moreover, short i is rendered at its logical position rather than where it ought to be, so in dghri, the short i marker follows the above sequence, attached to thin air.
All the best,
Daniel