I don't have a Harmony remote but AFAIK the selected remote profile is what defines the scancodes to be sent - so dig into that.
My guess is the remote profile sends two different scancodes on left/right to support two (slightly) different DVD players - which might work with the original players but is highly non-standard with anything else.
Check if there are other similar remote profiles if you want to stick to the Pioneer DVD profile or just configure the Harmony to use the Microsoft Media Center remote (not the MCE keyboard!), this will work out-of-the box in LE.
If you plan to use both your original pioneer remote and the Harmony to control LibreELEC you can still do this when the Harmony is configured as MCE: Enable both nec and rc-6 protocols in the keymap and add the key/scancode definitions from rc6_mce to your keymap (we do a similar thing in the default libreelec_multi keymap to support Xbox remotes in addition to MCE).
so long,
Hias