Ah, I can see what you are saying now. The rear glass is stuck as you said because some very small object has got caught and jammed the rear mechanism(can be as small as a tiny stone, a piece of the mechanism has broken jamming the rear or preventing the rear mechanism to contract back. However, it could be a completely different issue related to the installation of your new seal. Is this a seal that circles the whole panoramic roof? I am not sure how much of the rear rails/mechanism you can see at this stage to zoom in on the rail mechanism. Good luck with it.

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2005 X5 4.4i M Sport
2003 X5 4.4i