pt-table-checksum not finding differences
When you stop a slave the master has no idea what its slaves are. 
pt-table-checksum doesn't see your slaves.

pt-table-checksum is a mature tool and the most popular in the Percona toolkit. The data inconsistency is easy to reproduce. Just write something on a slave. By the way, there is a vagrant master->slave configuration in https://github.com/twindb/twindb_table_compare, you can test pt-table-checksum on it.

By default pt-table-checksum connects to localhost. Do you run it on the master? Can you connect to the slave with mysql client with same user/password?



There were two issues preventing the check from working correctly:


When replication is stopped on a slave, the master will not see it as a slave (and therefore not check it).
Permissions allowed pt-table-checksum to connect to the master, but not to the slaves (since that account was restricted to localhost). However, the tool will not show permission denied. Instead it just ignores the slave.