My first thought is the external files may have an "exit" in them. You don't need Tk to demonstrate this. Comment out the do and system lines in caller, and see the difference. Basically "do" runs the external script as if it where part of the caller, and if it hits an exit.....bye bye.

#caller
#!/usr/bin/perl
$|++;
print "start\n";

do "test";
#system ("./test");

print "done\n";
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#test
#!/usr/bin/perl
print "test\n";
exit;
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