Note: Completely rewrote this post as I got some sleep and have the code to demo the issue. Hoping you can now really see the cause/problem and offer ideas.

Thanks in advance!

PS: I think there some leaks etc in that code, but didnt care about those at this point.

myModule.xs

#include "EXTERN.h"
#include "perl.h"
#include "XSUB.h"

#include "ppport.h"

#include <pthread.h>
static PerlInterpreter *orig_perl=NULL;
static PerlInterpreter *cb_perl=NULL;

SV* cb_ptr = NULL;

void InvokeCB ()
{
   static int val = 0;
   val++;
   dTHX;
   dSP;
   ENTER;
   SAVETMPS;
   PUSHMARK(SP);
   SV * sv = cb_ptr;
   if (my_perl != orig_perl)
   {
      CLONE_PARAMS clone_param;
      clone_param.stashes = NULL;
      clone_param.flags = CLONEf_COPY_STACKS | CLONEf_KEEP_PTR_TABLE;
      clone_param.proto_perl = cb_perl;
      sv = sv_dup(sv, &clone_param);
   }

   XPUSHs(sv_2mortal(newSViv(val)));

   PUTBACK;
   call_sv(sv, G_DISCARD);

   FREETMPS;
   LEAVE;
}

void * BGThread(void * dontcare)
{
   PERL_SET_CONTEXT(orig_perl);
   cb_perl = perl_clone(orig_perl, CLONEf_COPY_STACKS | CLONEf_KEEP_PT
+R_TABLE);
   PERL_SET_CONTEXT(cb_perl);
   while (1)
   {
      sleep(5);
      InvokeCB();
   }
}

MODULE = myModule               PACKAGE = myModule

int
RegisterCB (SV *SubRef)
    CODE:
       pthread_t tid;
       pthread_create(&tid, NULL, BGThread, NULL);
       orig_perl = PERL_GET_CONTEXT;
       cb_ptr = newSVsv(SubRef);
       SvSHARE(cb_ptr);
       RETVAL = 1;
    OUTPUT:
       RETVAL
[download]

test.pl

#! /usr/local/bin/perl

use myModule;
use warnings;

#shared scalar
$cb_done = 0;
@results = ();

#This cb would be invoked by the cloned interpreter in the
#C library.  This works fine.
sub cb_one
{
  ($value) = @_;
   print "CB called. val received : ", $value, "\n";
   $results[scalar(@results)] = $value;

   if ($value == 5)
   {
      print "cb_done changed to one.\n";
      $cb_done = 1;
   }
}

print "Registered CB...\n";

$status = myModule::RegisterCB(\&main::cb_one);
do
{
   print "Waiting for CB to be done...\n";
   sleep (5);
} until ($cb_done == 1);

#These line should be printed when $cb_done becomes 1
#in the main of the perl script
print "CB was invoked : $cb_done\n";
print "results are : @results \n";
[download]

script output

Name "main::status" used only once: possible typo at ./test.pl line 27
+.
Registered CB...
Waiting for CB to be done...
Waiting for CB to be done...
CB called. val received : 1
Waiting for CB to be done...
CB called. val received : 2
Waiting for CB to be done...
CB called. val received : 3
Waiting for CB to be done...
CB called. val received : 4
Waiting for CB to be done...
CB called. val received : 5
cb_done changed to one.
Waiting for CB to be done...
CB called. val received : 6
Waiting for CB to be done...
CB called. val received : 7
[download]