Instead of choosing the table by header, try to chose by attrib:

#    headers =>[qw(RefSNP)]);
    attribs => { id => "RefSNP" } );
[download]

For me this worked, when applying it to the source of

http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=rs111
[download]

The output still contains a lot of HTML.