I've been having the same issue. But after spending some time on it, I think I'ev figured out the problem:
Spigot is not writing the proper NBT data to the level.dat when the server is shut down.

There's a "DimensionData" folder under "Data" that stores information pertaining to The End; if the dragon is currently dead, how many times it was killed prior, gateway coordinates, etc. When I moved the level.dat off my server and dug into it, I found the DimensionData folder was entirely empty. I injected the proper data to that .dat by remaking the world in SSP (ie. dragon still alive, no previous kills). When I boot up the server, this resutls in the dragon always being alive, and the crystals properly working to respawn it... but it, of course, still fails to write to the data on server-stop, so it never remembers how many times I've killed it during uptime.

I can set it on fire with flint. I doubt that is the problem (no protections on). I am not getting flames when placing them in the proper spots.

I have fire effect, still no change. Check your plugins for fire protection maybe?

Can confirm this is happening, on newly generated worlds and old worlds as well. The fire effect that should occur when placing an end crystal does not occur for any crystal placed.