Starting in 2009, the University of Twente uses Blackboard as on-line learning management system. However, Blackboard turns out to be very insecure; see for instance the news item (in Dutch) Universiteitssoftware blijkt langdurig lek. Among other things, it is not only possible but actually easy for students to hack into a teacher's account and invisibly change grades. As it turns out, this has been known amongst our students for quite some time.
Blackboard is a commercial system and its internals are a company secret. Kerckhoff's Principle states that a secure system must not require secrecy. This way, it can be stolen by the enemy without causing trouble. In the design of software systems, this argument is used in favour of open source software security: Security through obscurity is considered bad practice, see for instance Jaap-Henk Hoepman and Bart Jacobs' Communications of the ACM article Increased security through open source (CACM 50-1, 2007). So, maybe it is time to look at some of the open source alternatives out there, such as Sakai or Moodle. Both come with commercial support, in case our technical university does not want to invest in the expertise to deploy such a system in-house.