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This problem is addressed in ArcGIS 8.1 Service Pack 1. See the Related Information section to download this pack.
ArcScene can take a long time to exit when there's a lot of data in the scene and/or many layers.
There are two possible causes:
One is the 'Save thumbnail image' option. When turned on ArcScene rerenders all the data to an off-screen rendering context to create the image thumbnail. This can take a long time when a lot of data is present in the scene.
The other cause is when there are many layers present and the TOC refreshes excessively.
Turn off the 'Save thumbnail image' option from the Document Properties dialog found under the File menu.
There is currently no solution if the slowdown is related to excessive TOC refreshes.