proper prolog command-line instead of hashbang, which might switch to invalid executable and thus fail (notably on lxbroy2);
speculative update for yap (untested);

--- a/src/HOL/Tools/Predicate_Compile/code_prolog.ML	Mon Apr 15 22:51:55 2013 +0200
+++ b/src/HOL/Tools/Predicate_Compile/code_prolog.ML	Tue Apr 16 17:54:14 2013 +0200
@@ -750,7 +750,6 @@
     "\\n', [" ^ space_implode ", " vnames ^ "]), writelist(SolutionTail).\n"
   
 val swi_prolog_prelude =
-  "#!/usr/bin/swipl -q -t main -f\n\n" ^  (* FIXME hardwired executable!? *)
   ":- use_module(library('dialect/ciao/aggregates')).\n" ^
   ":- style_check(-singleton).\n" ^
   ":- style_check(-discontiguous).\n" ^
@@ -766,7 +765,6 @@
   "\\n', [" ^ space_implode ", " vnames ^ "]).\n"
 
 val yap_prelude =
-  "#!/usr/bin/yap -L\n\n" ^
   ":- initialization(eval).\n"
 
 (* system-dependent query, prelude and invocation *)
@@ -786,7 +784,7 @@
   let
     val (env_var, cmd) =
       (case system of
-        SWI_PROLOG => ("ISABELLE_SWIPL", "\"$ISABELLE_SWIPL\" -f ")
+        SWI_PROLOG => ("ISABELLE_SWIPL", "\"$ISABELLE_SWIPL\" -q -t main -f ")
       | YAP => ("ISABELLE_YAP", "\"$ISABELLE_YAP\" -L "))
   in
     if getenv env_var = "" then