Are you sure your Harmony is set up right? In general it's recommended to configure the Harmony remotes to use the Microsoft Media Center (MCE) remote profile (NOT the MCE keyboard profile!), then it'll work out of the box with LE (you only need to add the dtoverlay=gpio-ir line to config.txt).
If in doubt simply run ir-keytable -p all -t, that'll show scancodes of all supported protocols that the IR receiver saw. If you don't see anything from your Harmony remote, look at the Harmony config.
so long,
Hias