Hi,

If I put the Dna-SNP.svg file in the current directory, it works fine:
     \starttext
     %\setupexternalfigures[directory=figure]
     \externalfigure[Dna-SNP.svg]
     \externalfigure[Dna-SNP.png]
     \stoptext

If I put the Dna-SNP.svg file in the figure subdirectory, then it broke:
     \starttext
     %\setupexternalfigures[directory=figure]
     \externalfigure[Dna-SNP.svg]
     %\externalfigure[Dna-SNP.png]
     \stoptext

And If I convert the Dna-SNP.svg in the figure subdirectory into 
Dna-SNP.png, and comment the .svg line, while uncomment the .png line, 
it works again.

So the problem is that \externalfigure can't find svg files in the path 
specified by \setupexternalfigures.

Dna-SNP.svg is attached in case somebody want to test it.