Does the DNA or RNA of some ethnic groups map better than others' to the human reference genome sequence?
For simple variants like SNPs it would not really be a problem to use the current genome assembly for other ethnic groups. But for more complex variants this could be indeed problematic, however not only for ethnic groups but also for individuals within the same population. Think of very complex regions such as HLA or KIR.

In studies where they compare different ethnic groups (e.g., 1000 G) they rather not discuss such matters, but act like the analysis is 100% perfect.

There is a nice comment in Genome Biology about this issue.