Sorry for the delay. Our solution was to just rip it out entirely instead of fighting with it.
I've needed a solution like this for other applications, so I took a look at the code you suggested. IPC::Run3 does seem to work, but I couldn't figure out how to connect to it. There are no examples at all and no one seems to use it. I tried setting up pipes for it, but nothing is returned when I do that:
use IPC::Run3;
use IO::Pipe;
my $cmd = "cmd /D/C dir";
my $out = new IO::Pipe; $out->reader();
my $err = new IO::Pipe; $err->reader();
run3 $cmd, $out, $err;
print "OUT: $out ERR: $err\n";
map {print "$_\n"}<$out>;
map {print "$_\n"}<$err>;
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