I think the problem lies because you were upgrading from 1.1beta. If you look in search.cgi you'll see:

print "\nCreating Search Indexes ... ";
eval {
my $DB2 = new Links: BSQL '../defs/Links.def';
$DB2->create_index();
$DB2 = new Links: BSQL '../defs/Category.def';
$DB2->create_index();
};

This should create the search indexes for you. If you are starting with an empty database, then when you create the table, the indexes should be created automatically.

I'll work on polishing the setup a bit more and making it a little smarter.

Cheers,

Alex