Both the remotebackend and bindbackend use sources from
the pdns/ directory two levels up.
When running make distclean, the automatically generated
dependencies are cleaned from the current directory.
When make next recurses into pdns/, those .deps are gone
and make fails.
http://debbugs.gnu.org/cgi/bugreport.cgi?bug=17354 describes
the same issue.
The obvious fix (apart from fixing the bug in automake) is
to either switch to non-recursive make, or create a convenience
library.
Until that hapens, disabling dependency tracking is the only
solution I see. The nice side effect is that this speeds
up one off builds tremendously.