Know this is an old thread but just wanted to add my data point to it.
I have a 6S on 14.4 and was getting the missing overlay issue. Worked at first and then stopped appearing.
I've noticed that I only get the issue when jailbreaking using checkra1n on my ra1nbox (mini linux box similar to Raspberry Pi)
If I rejailbreak using checkra1n on my laptop (with checkn1x), the overlay comes back. Rejailbreaking with ra1nbox makes it disappear again. Both are have latest checkra1n (12.2 beta).
Dunno know if that helps or if the cause of the issue is already known, but thought I'd share.
~John