Strange. This may have something to do with the BTree implementation in the version of DB_File you have. You might try upgrading your libdb to a later version (this is something you'd do through your OS tools) and upgrading to the latest BerkeleyDB release from CPAN (which includes the latest DB_File).

There is also a way to change the cache size that it uses, although you may need to use the API from the the BerkeleyDB module rather than the DB_File one to do it.

If your keys are small enough, SDBM_File can be faster than DB_File. It has size limitations though.