I've seen reports of this, for example here:
https://lists.gnu.org/archive/html/lilypond-devel/2016-09/msg00045.html
I have the same issue on OSX 10.12.3, using 2.19.48-1
From running with --verbose, I see it is rebuilding the font cache each
time. I tried various things like checking permissions and also removing the
font cache to see if it would like it if were rebuilt with 2.19. But it
also didn't have an impact.
2.18.2-1 doesn't have this issue.
Would it be appropriate for me to add this as a bug in the sourceforge
page? It does not result in incorrect output, just an extremely long run time
while it rebuilds the cache. For example, 50 seconds vs 2 seconds.