I experience the same as Paul

autoconf (GNU Autoconf) 2.61
GNU Make 3.81

autoconf
make -j3
.
.
gcc -march=i686 -mtune=generic -O2 -pipe  -fPIC   -I. -I.ext/include/i686-linux -I./include -I.  -DRUBY_EXPORT -D_GNU_SOURCE=1   -o dmyext.o -c dmyext.c
./miniruby -I./lib  ./enc/make_encdb.rb ./enc encdb.h
make: ./miniruby: Command not found
make: *** [encdb.h] Error 127
make: *** Waiting for unfinished jobs....


unfinished jobs are :

29802 pts/1    S+     0:00 make -j3
29885 pts/1    S+     0:00 gcc -march=i686 -mtune=generic -O2 -pipe -fPIC -I. -I.ext/include/i686-linux -I./include -I. -DRUBY_EXPORT -D_GNU_SOURCE=1 -o parse.o -c parse.c
29886 pts/1    R+     3:10 /usr/lib/gcc/i686-pc-linux-gnu/4.3.0/cc1 -quiet -I. -I.ext/include/i686-linux -I./include -I. -DRUBY_EXPORT -D_GNU_SOURCE=1 parse.c -quiet -dumpbase parse.c -march=i686 -mtune=generic -auxbase-strip parse.o -O2 -fPIC -o -
29887 pts/1    S+     0:00 as -Qy -o parse.o -

when done ...

ls -lRt |head -n 5
.:
total 8728
-rw-r--r--  1 jeyzu users     222848 2008-04-02 07:57 parse.o
-rw-r--r--  1 jeyzu users      71968 2008-04-02 07:43 vm.o
-rw-r--r--  1 jeyzu users        667 2008-04-02 07:43 dmyext.o

make -j3
gcc -march=i686 -mtune=generic -O2 -pipe  -fPIC   -I. -I.ext/include/i686-linux -I./include -I.  -DRUBY_EXPORT -D_GNU_SOURCE=1   -o compile.o -c compile.c
gcc -march=i686 -mtune=generic -O2 -pipe  -fPIC   -I. -I.ext/include/i686-linux -I./include -I.  -DRUBY_EXPORT -D_GNU_SOURCE=1   -o iseq.o -c iseq.c
./miniruby -I./lib  ./enc/make_encdb.rb ./enc encdb.h
make: ./miniruby: Command not found
make: *** [encdb.h] Error 127
make: *** Waiting for unfinished jobs....

ls -lRt |head -n 5
.:
total 8848
-rw-r--r--  1 jeyzu users      75116 2008-04-02 08:04 compile.o
-rw-r--r--  1 jeyzu users      44144 2008-04-02 08:04 iseq.o
-rw-r--r--  1 jeyzu users     222848 2008-04-02 07:57 parse.o

make -j3
gcc -march=i686 -mtune=generic -O2 -pipe  -fPIC   -L.  -rdynamic -Wl,-export-dynamic   main.o dln.o dmyencoding.o dmytranscode.o miniprelude.o array.o bignum.o class.o compar.o complex.o dir.o enum.o enumerator.o error.o eval.o load.o proc.o file.o gc.o hash.o inits.o io.o marshal.o math.o numeric.o object.o pack.o parse.o process.o prec.o random.o range.o rational.o re.o regcomp.o regenc.o regerror.o regexec.o regparse.o regsyntax.o ruby.o signal.o sprintf.o st.o string.o struct.o time.o util.o variable.o version.o blockinlining.o compile.o debug.o iseq.o vm.o vm_dump.o thread.o cont.o id.o ascii.o us_ascii.o unicode.o utf_8.o strlcpy.o strlcat.o  dmyext.o  -lpthread -lrt -ldl -lcrypt -lm   -o miniruby
./miniruby -I./lib  ./enc/make_encdb.rb ./enc encdb.h
make: ./miniruby: Command not found
make: *** [encdb.h] Error 127
make: *** Waiting for unfinished jobs....

bigdaddy jeyzu trunk $ ls -lRt |head -n 5
.:
total 10384
-rwxr-xr-x  1 jeyzu users    1565487 2008-04-02 08:05 miniruby*
-rw-r--r--  1 jeyzu users      75116 2008-04-02 08:04 compile.o
-rw-r--r--  1 jeyzu users      44144 2008-04-02 08:04 iseq.o

obviously next run is the good one 

-- 
Zurcher Jérémy
rte. Cully 29
1091 Grandvaux
http://tzurtch.pas.nu
+41 (0) 79 599 84 27