According to the DBI man page:

If there are no more rows or if an error occurs, then "fetchrow_array" returns an empty list. You should check "$sth->err" afterwards (or use the "RaiseError" attribute) to discover if the empty list returned was due to an error.

So, have you tried that?

Apart from that, if there are "other changes we've made", maybe it's sufficient that you don't see any "reasonable correlation" to your troubles, but maybe someone else might see something you missed... We won't know unless you tell us a little more about those changes (and any possibly relevant differences between this failing script and your separate DBI script).