I faced the exact same problem you faced when I first changed the cabin filters. No amount of work would get the gasket to sit flush on the glass.

Right uptil I cleaned the groove and use dishwash soap to aid the rubber seat into the groove. Otherwise it just sat proud of the glass.

For using sealant - if you silicone this, then forget any repair you will need to do like cabin filter or AC expansion valve.

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2012 BMW X5 (Beef + Granite suspension model)

1995 E300D - The original humming machine (consumed by Flood 2017)
2000 E320 - The evolution (consumed by flood 2017)