the conversion still works fine, but for each file I also get the following msg

Where does the message come from? The snippet of code you've shown doesn't seem like the cause (update: try to find the exact line). Try adding

use strict;
use warnings;
use diagnostics;
[download]

and see if that helps you narrow it down. If it doesn't, try to use Devel::Trace.

update: HTML::TextToHTML has a debug option, that might also help you narrow it down (might be easier than using Devel::Trace).