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Got the solution eventually, I'll post it here in case anyone else runs into a similar problem:
The dll files of opencv installed onto the server which hosted the web app had different access rights. The files were denied access when being called from the web application, whereas the rest of the modules called had no issue.
I used sysinternals process monitor to trace which files were being denied access and was able to change the rights by hand. Not very elegant but it worked out.
