This has been the case for as long as i can remember. SD is set to standard 3 degree glide path but the glide almost always shows fly down even if perfectly aligned on the actual GP. Towards the later stages of the approach it vanishes altogether.

Any‌ suggestions on the cause?

https://www.instagram.com/liam548/

Look at the actual altimeter reading in SkyDemon at an exact position. You can double-check the reading once you've got that. Chances are, your GPS is giving you a different altitude than your pressure altimeter in your aircraft, which explains the discrepancy. GPS altitude is notorious for such inaccuracies in the vertical plane.