Non-Replicating commands from (master) Mysql 5.5.40 to (slave) MariaDB 10.0.19
USE db_99;
do something with db_1 or 2 or 3;


will not replicate because of your binlog-do-db and replicate-do-db.  (The latter is redundant in your case.)

This is because replication (except for "wild" versions) is based on the USE, not on any explicit db spelled out in the statement.

Is it a "bug"?  Well, a lot of people get burned by it.