I will see what I can do.

Please test the attached patch, which reads output from latex
immediately after they are available.

Cheers,
Bo
Index: lib/configure.py
===================================================================
--- lib/configure.py	(revision 14498)
+++ lib/configure.py	(working copy)
@@ -553,9 +553,14 @@
         cl.close()
         #
         # we have chklayouts.tex, then process it
-        for line in cmdOutput(LATEX + ' wrap_chkconfig.ltx').splitlines():
+        fout = os.popen(LATEX + ' wrap_chkconfig.ltx')
+        while True:
+            line = fout.readline()
+            if not line:
+                break;
             if re.match('^\+', line):
-                print line
+                print line,
+        fout.close()
         #
         # currently, values in chhkconfig are only used to set
         # \font_encoding

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