( Not sure whether I have correctly digested every bit of information you supplied (quite a lot to read :) -- so in case I misinterpreted something, just ignore my post...)

You are aware that symbols are exported only into the namespace of the module from which the use is being issued, are you?

A simple example. Assume the following definitions

package X;

require Exporter;
our @ISA = qw(Exporter);
our @EXPORT = qw(func_in_X);

use Y;

sub func_in_X {
    print "func_in_X called.\n";
}
1;

---

package Y;

require Exporter;
our @ISA = qw(Exporter);
our @EXPORT = qw(func_in_Y);

sub func_in_Y {
    print "func_in_Y called.\n";
}
1;
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Now, if you only use X in your script:

#!/usr/bin/perl

use X;   # X uses Y secondarily

# this works
func_in_X();     # imported into our namespace
Y::func_in_Y();  # fully qualified 
X::func_in_Y();  # fully qualified via namespace X,
                 #   into which func_in_Y() has been exported

# this doesn't work
func_in_Y();     # not imported into our namespace
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A simple way around this is to explicitly use every module, of which you need any symbols in your current namespace.