I experienced that, after a scheduled Titanium Backup backup, some apps (WhatsApp, Telegram, K-9 Mail, maybe others) doesn't appears to be running any more, i.e. I don't receive notifications from them. I have to open them to restore their functionality. Even a device reboot doesn't resolve the problem. This doesn't happen with other apps. Gmail, for example, continues to work.
This happen when the setting app advanced control from backup section is disabled, i.e. apps are killed instead of suspended and restored during a backup. May be that Android fail to restart the killed apps, or a behavior of the apps that prevent them to be restarted.
I have a Lenovo K50-t5 and tried with the ROW-1552D ROM, Android 5.1, customized by cuoco92, and with the Android 6 release.