It seems you never got an answer. Here a late one. In a lot of applications the account name of a Mendix application is the user mail adress. Problem is that email@example.com is for email purposes the same as Ronald.Catersels@somemail.nl but when talking about account names these will be two different accounts. Hence the option to do the check for an account in lowercase. Now to enable (or disable) this check the resources folder for the SAMLConfig.properties file. Here you will see this:
#When evaluating the usernames should the PrincipalValue (username) be altered to a lowercase value, basically resulting in case-insensitive search? #not specifying this options keeps the old implementation #DEPRICATED, in the Mx7 release this property becomes mandatory with default=true sso.principalvalue.tolowercase = true
So setting this to false would probably solve your case.