When you change the scenario this way:

0) ./configure
1) make
2) make
3) make install

then the second make does the rebuild, and the "make install" works correctly.

So it's not the case that src/gnm-marshalers.c is constantly rebuilt, it's
rebuilt only once.

An analysis:

To create gnm-marshalers.lo, make has to use the following two implicit rules:
.list.c:
.c.lo:

Then gnm-marshalers.c is so called "intermediate file", and make deletes it as
soon as gnm-marshalers.lo is created.  So the first run of make in fact doesn't
create gnm-marshalers.c.

But the first run of make creates file .deps/gnm-marshalers.Plo.  That file
specifies the dependency
gnm-marshalers.lo: gnm-marshalers.c

In the next run of make, .deps/gnm-marshalers.Plo is included by the Makefile.
In this file, gnm-marshalers.c is mentioned explicitely as a prerequisite: this
means that it can no longer be treated as an "intermediate file", and since it
doesn't exist, it has to be created.

Thus it is created, and all targets depending on it have to be refreshed.

There are several possible ways to fix the problem.

For example, it's enough to add the following rule:
gnm-marshallers-dummy: gnm-marshallers.c

Since the file is mentioned explicitly as a prerequisite, it will never be
treated as an "intermediate file".

Another solution is to add the gnm-marshallers.c to BUILT_SOURCES. 
(BUILT_SOURCES are prerequisities of the targets "all", "check" and "install".)

Though the former solution is more elegant, the later one has the advantage that
it also fixes bug #172212, so I commit it.

IMHO, the most elegant solution is to add the rule

gnm-marshallers-dummy: gnm-marshallers.c

Since the file is mentioned explicitly as a prerequisite, it will never be
treated as an "intermediate file".

Oops!  Please forget Comment #3.

The solution from Comment #4 seems to fix bug #172212, too.
So I'm going to use it.