OK, I've reduced my observed problems with index generation to a simple test case:

\starttext

\placeindex

\page

\index{one}whatever % Shows up [1]

\index{one+sub}whatever % Shows up correctly as sub-entry

\index{two}whatever % Shows up [2]

\index{one}whatever % Skipped because duplicate of [1]

\index{two}whatever % Shows up as a duplicate of [2]

\index{three}whatever % Doesn't show up at all

\stoptext

So, both duplicate entries and missing entries. It could be that having a mixture of 1-level and 2-level index entries isn't supported, but it *used* to work... Unfortunately I hadn't updated my ConTeXt install in months, so I can't tell when it broke.

mathew