I have also this problem. My core 3.0.3.
[12-Oct-2012 12:34:05 UTC] MDB2 Error: unknown error (-1): _doQuery: [Error message: Could not execute statement]
[Last executed query: PREPARE mdb2_statement_mysql_2b8993aba2a98583f78fe8761f3db6b76c25f7886 FROM 'INSERT INTO session (sess_id, vars, ip, created, changed) VALUES (?, ?, ?, \'2012-10-12 14:34:05\', \'2012-10-12 14:34:05\')']
[Native code: 1286]
[Native message: Unknown storage engine 'InnoDB']
[12-Oct-2012 14:34:05 +0200]: DB Error: _doQuery: [Error message: Could not execute statement]
[Last executed query: PREPARE mdb2_statement_mysql_2b8993aba2a98583f78fe8761f3db6b76c25f7886 FROM 'INSERT INTO session (sess_id, vars, ip, created, changed) VALUES (?, ?, ?, \'2012-10-12 14:34:05\', \'2012-10-12 14:34:05\')']
[Native code: 1286]
[Native message: Unknown storage engine 'InnoDB']
in /usr/share/roundcube/program/include/rcube_mdb2.php on line 293 (GET /webmail/)
Please help me! Thanks. J. Rok