When building CTDB and using the --prefix option the generated system is improperly configured.
The build system assumes the CTDB is to be installed at /, and when the --prefix statement is used generates incorrect paths, i.e.
the Makefile that generated assumes that
ETCDIR = /usr/local/ctdb/etc/ctdb
Which if you run the "make showlayout" does not match.
This error is also hard coded into the ctdbd.c options list.
This is properly fixed in CTDB in Samba >= 4.4. It is too invasive to backport.
Some of these issues were fixes in earlier versions but the fixes in 4.4 are comprehensive.