Under Ubuntu 9.04, I installed DBD::SQLite from CPAN (http://search.cpan.org/~adamk/DBD-SQLite-1.30_02/) and got the error “The database disk image is malformed”.
This error only occurred when running Perl on a database created with sqlite3, but not sqlite.
I ran repair tools on the database and created new databases with only one entry and still got the error.
The solution was to uninstall DBD::SQLite from CPAN and install the package that comes in Ubuntu 9.04 libdbd-perl-sqlite3.
I am now able to run Perl on a sqlite3 database using DBD::SQLite.