Can you try this patch, please? It has the same effect as the other
patch from Neal but it doesn't loose ref counts. I've patched the
dealloc function of _FileIO to keep fd 1 and fd 2 open.

Index: Modules/_fileio.c
===================================================================
--- Modules/_fileio.c   (Revision 58699)
+++ Modules/_fileio.c   (Arbeitskopie)
@@ -270,7 +270,8 @@
        if (self->weakreflist != NULL)
                PyObject_ClearWeakRefs((PyObject *) self);

-       if (self->fd >= 0) {
+       /* Don't close stdout and stderr */
+       if (self->fd == 0 || self->fd > 2) {
                errno = internal_close(self);
                if (errno < 0) {
 #ifdef HAVE_STRERROR