When I was reading the original post and replies, it only strengthens me in
my believe that no only you are struggling with the problems proprietary
software brings along, but it also appears that you are caught by "modern"
politics. It appears to me that your university, similar to other
universities in Europe, is ran like a business rather than a place to really
gather understanding and knowledge about the science itself.
The knowledge has declined the past decade from being excellent to mediocre,
to say the least, let alone the understanding that they should teach you what
computer science is (whether it's bachelor or master doesn't matter), rather
than teaching you one or the other software component or language.
I have my own experience with this nonsense, as I was forced to learn Java in
a Sybase environment. The only difference was that my teachers where as
dissatisfied as I was myself.
I believe the Free Software movement needs to be much stronger in Europe
(which is a truly proprietary dominated area).
I hope you will be able to change things mildly, and try to find allies, even
if they are so few, to guide you.