I cannot adequately comment on the coredump. I do think the $value = $$value causes issue -- in my mind, you're saying that \$value = $value; Or, pointer to memory location of $value = content of memory location of $value. Nevermind that $value is a scalar, not a scalar ref, to begin with. What I don't really understand is the ($value) = ($$value) bit. Why using list syntax lets this work is for others more experienced than I to answer. But hey, whatever works...

I would, however, suggest one thing. As opposed to reading the text, then using eval to "perlfy" it, why not do something like this:
Change your current "config.txt" to "config.pl", and rewrite thusly:

$stored_proc_list = [(qw(sproc1 sproc2 sproc3))];
$update_stats_xref = {sproc2=>"update_table2"};
$logfile = "somefile.txt";
1;  #Return true val
[download]

Then just require it. All of your vars then get populated without using the eval.