Yes it appears briefly right as the camera pans past the listening post and escorts a tanker toward the Cerberus.
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I know its related to the Excalibur because there are only two upgraded models in the scene (currently) the Panther and Excalibur. When the game started crashing I replaced the models with their originals and it worked fine, by process of elimination I discovered it to be the Excalibur that was causing the crash, darned if I know why though.
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As for the cockpit meshes, funny you should mention that. @Dark Sentinel wants to look into tinkering on an upgraded Panther cockpit for the mod.
I don't know what that could be caused by, but I took a look at the original Excalibur model in a hex editor, and it has a BSP tree and REGN/BLCK forms for some reason.