No, they are not case sensitive.
The Whitelist entry form doesn't let me enter the same name twice regardless of case. For example, if I add "@testdomain.com", then try to add "@TESTDOMAIN.com" it says "The specified address is already included in the list".
Quite some time ago domains were entered without the leading "@" but now you have to enter the leading "@" to specify the domain only. If your old entry was without the "@" then it would allow you to enter it again with the "@" regardless of case.
We would need to look at the message headers to determine why it might have been flagged as spam an not whitelisted.
Could you please submit a Support Ticket at
https://support.runbox.com and identify the message (date, subject, folder) in your account for us so we can investigate the cause.
Regards,
Rich