Thanks for sending me a test dataset.

I've confirmed that my beta utility does indeed fall short in handling those specific fields. Haven't determined "why". BUT there is a good workaround.

I tested a_berezin's convert_db2utf8.php utility http://www.zen-cart.com/downloads.php?do=file&id=1318 and it handles the data just fine. (It uses a different conversion strategy, which puts the onus on the MySQL server to do all the conversion logic, instead of on PHP like mine did.)
So, I'm recommending that a_berezin's utility be used instead of mine.

I also just posted an update to a_berezin's plugin to make it compatible with PHP 5.4-5.6