After getting the second orb, a messenger came running, telling me that I need to meet the professor at the Library. A savepoint appeared, and I saved (overwriting my last save...). Well, something seem to have failed to trigger, because when I fast travel to the library, it is empty, no professor is there to greet me and tell me what to do next.
Has anyone else encountered this problem, and is there a known workaround for it?

first a quest and a solution
first of all did you rescute the professor from the imp when you first entered it in that case you need to do that before he comes down here on that even

when you first enter there you go up and in the library almost at the top there are 2 doors the one on the right continue futher up until you reach the wicked magician hte other is a deadend where he is with a few ims running around and a mage imp summoning more imps

It was a while ago since I posted this, but if my memory serves me yes, I did rescue the professor and defeated all the imps. Don't you have to do that in order to get to the part where you look for the orbs?

nope you can go straight right and continue if i was you i would check, if he is not rescued then you got the reason he is not there

and remember to trigger the event you have to enter the library from the main entrance where you first came in and not from the telescope etc.