Bart,
I know it's in unicode now, but I think the problem was that MySQL still assumes that it's in latin1 -- when you upgrade to MySQL 4.1, as I understand it, some of the text is "converted" to unicode which can mess things up that are already in unicode. I saw on http://peter-zaitsev.livejournal.com/12083.html "If you will configure MySQL 4.1 to use utf8 by default and just start it with MySQL 4.0 latin1 tables you're likely to trash your data, as there is no charset information in old tables and MySQL 4.1 will assume the data is in unicode. So do not change character set straight ahead but run 4.1 with same charset as 4.0 before and use ALTER TABLE to convert tables to 4.1 format - this has character set information so you should be safe."
Or you can use --character-set-server (=binary in our case).
Cheers, Domas