There are two possible issues I can think of that might be causing this problem.
1. You have a load balancer in front of Orion websites. You need to configure the load balancer to make sure that it keeps sending requests as part of the same session to the same Orion webserver. Otherwise you could be mixing sessions.
2. You have your IIS set up for multiple worker processes. Under 2008, this is part of the Application Pool/Advanced Settings. You should make sure your Maximum Worker Process value is set to 1. The end result is the same as above, mixing of sessions.
If those aren't it, please open up a support ticket and we'll get this tracked down for you.
Thanks for your input Casey!
1. There is no loadbalancer involved, but the server connects over 2 interfaces in teaming mode.
2. I've verified the multiple worker processes: it was already set to 1
As a despreate measure I have now disabled the user account which interferes. If the issue still arises I will act on your advice and open a support ticket.
In case anyone should experience the same problem:
After spending some more time on this I discovered, that on the pages (where I tried to unmanage a node) is a chart that is created using Custom HTML. The HTML code used a different user and password (for whatever reasons) to generate the chart. This fact was revealed when I disabled the user in question. I removed the user and password from the HTML code.
Since then I haven't had any more troubles.