What kind of mySQL version do you use?
Your problem seems very specific and unfortunately without deep debugging, I can't say what's wrong. Whatever I can say the problem belongs to your mySQL settings or something else on your side... On miniBB demo
page we have $loginsCase=TRUE;
and as you may see, this setting works from all aspects... so you can register some user name containing both uppercase and lowercase, then log-in using lowercase only, and it works.
On your server, there is something strange, because when I register something in uppercase/lowercase, and if that setting is set to TRUE, then I can log-in only with lowercase... not with my original user name.