I found the problem.
Even in Linux DBD::SQLite was crashing perl.
There's a note in the SQLite's webpage that the format of the database was changed in recent versions.
I was creating the database using the sqlite tool, and it was the last version, generating a database incompatible with the library that comes with DBD::SQLite, making perl segfault.
Updating the module from CPAN works, and for WIndows, updating from the theory5 (http://theoryx5.uwinnipeg.ca/cgi-bin/ppmserver?urn:/PPMServer) ppm repository seems to work with a recent sqlite tool.

Update: If you cannot update the module, creating and managing your database with dbish may work. Do NOT open the database with a recent sqlite tool, because it will be upgraded automagicaly.
The syntax is: dbish DBI:SQLite:database.db