If you want Bioperl specific help you should probably post this question to the bioperl list since people who are interested in the toolkit tune in for similar questions.

To answer the question. It appears that your BLAST output contains something outside of what is expected by SearchIO. Are you reformatting the report after it comes out of the program before it is sent back via the RID process. Presumably you need to set up your cgi so it doesn't print anything that is not part of the BLAST format.

You can simulate all of this by taking the website out of the equation and just saving the report out to a file on the webserver. Then parsing it directly with Bio::SearchIO. If you run with -verbose => 1 you'll get more reporting of what the unrecognized data is. Presumably you have some sort of comments at the bottom of your report one of which contains 'genome' which is not parsing by the report.