This problem occurs when you stubify a file that is not in the current 
directory.  The file gets given the extension .000 instead of .exe.
If the file is renamed to a .exe it runs fine.  I have only observed this bug 
when stubify is called from a makefile,  I will try it from the command
line.  Also I have only tried it with lines of the form:
 stubify ..lahlah.foo

i.e directories before the current.  I will try it with lower dirs also.

Simple and obvious - rename the file yourself.  This is not very
good for makefiles,  though.

This bug ONLY occurs in the following situation:

the file to be stubified is in another directory at or below your directory
reachable only by going up a level first.  In the directory with the file
to be stubbed is an allready stubbed version.  The stubbed version is 
overwritten by the correct file but with an extention of ".000".  Renaming 
the .000 to .exe produces the correct file.  In all other cases I tested,
stubify correctly overwirites the .exe file with the correct file extention.

just change your makefiles from the V 1ish pattern of:

gcc file -ofile.foo
coff2exe file.foo
del file.foo

to:

gcc file -ofile.foo
del file.foo

(the exe is generated for you)