"I will be careful to use aliases in trigger command" - no, not a bug, "command" gets sent straight to the game (see tooltip). Just confusing design.
You raise a good point about trigger states. When modules are synced, they're uninstalled and reinstalled - so 'sysSyncUninstallModule' and 'sysSyncInstallModule' should be raised for the module. Try using that to reset the trigger states to what they should be?