Hard to fully diagnose without also seeing the actual cron. If you use a fully qualified path from the cron to mkvdts2ac3, when calling it, and use an absolute path to mkvmerge, when calling it from mkvdts2ac3. There should really be no problems.

OTOH are these shell scripts, or Perl scripts? Makes a big difference. Given this is a Perl related web site. I'll have to assume they're Perl scripts. In which case, divulging their code, or at least the relevant portions may better shed some light. That way, allowing someone here an opportunity to provide informative advice.

In any case, you'll probably need to effectively export a minimal $PATH to the script(s). In order to squelch the error.

Best wishes.

--Chris

#!/usr/bin/perl -Tw
use Perl::Always or die;
my $perl_version = (5.12.5);
print $perl_version;