You can try reenabling it at the end of beacon--vanish.
That worked!

But here's another idea: try adding this line inside
beacon--ov-put-after-string, between the two calls to `overlay-put'
    (overlay-put overlay 'priority most-positive-fixnum)

​I commented out the fci-mode hacks, did the above and re-evalled.. this works even better! Thanks!​

I didn't quite understand why setting the beacon overlay priority to the max worked.. Was it that earlier the fci-mode overlays were fighting to get displayed inbetween the beacon overlay displays? 

--
Kaushal Modi

On Thu, Oct 15, 2015 at 6:13 PM, Artur Malabarba <bruce.connor.am@gmail.com> wrote:
2015-10-15 22:44 GMT+01:00 Kaushal Modi <kaushal.modi@gmail.com>:
> OK, I think I need to reenable fci-mode at the end of beacon--dec. It seems
> to sort of work, just that the fci-mode gets re-enabled too soon, slightly
> before the beacon trails finish vanishing.

You can try reenabling it at the end of beacon--vanish.
But here's another idea: try adding this line inside
beacon--ov-put-after-string, between the two calls to `overlay-put'
    (overlay-put overlay 'priority most-positive-fixnum)