$ perl ./mtr sys_vars.secure_file_priv --mem
Logging: ./mtr  sys_vars.secure_file_priv --mem
vardir: /home/elenst/maria-5.5/mysql-test/var
Checking leftover processes...
Removing old var directory...
Creating var directory '/home/elenst/maria-5.5/mysql-test/var'...
 - symlinking 'var' to '/dev/shm/var_auto_37xY'
Checking supported features...
MariaDB Version 5.5.29-MariaDB-debug
Installing system database...
 - skipping ndbcluster
 - SSL connections supported
 - binaries are debug compiled
Collecting tests...
Using server port 38181

==============================================================================

TEST                                      RESULT   TIME (ms) or COMMENT
--------------------------------------------------------------------------

worker[1] Using MTR_BUILD_THREAD 300, with reserved ports 16000..16019
sys_vars.secure_file_priv                [ fail ]
        Test ended at 2013-01-21 16:08:46

CURRENT_TEST: sys_vars.secure_file_priv
/home/elenst/maria-5.5/client/mysqltest: Error on delete of '/home/elenst/maria-5.5/mysql-test/var/mysqld.1/data//../../../bug50373.txt' (Errcode: 2)
mysqltest: At line 19: command "remove_file" failed with error: 1  my_errno: 2  errno: 2

The result from queries just before the failure was:
< snip >
# Bug50373 --secure-file-priv=""
#
CREATE TABLE t1 (c1 VARCHAR(50));
INSERT INTO t1 VALUES ("one"),("two"),("three"),("four"),("five");
SHOW VARIABLES LIKE 'secure_file_priv';
Variable_name	Value
secure_file_priv	
test/var/mysqld.1/data//../../../bug50373.txt
c1
one
two
three
four
five
loaded_file
NULL

More results from queries before failure can be found in /home/elenst/maria-5.5/mysql-test/var/log/secure_file_priv.log