You say "by enabling single sceneries". By this do you mean switching every area off using the tick option in the Scenery Library then switching each on to see if the problem occurs. In other words the scenery cache only tries to regenerate those sceneries that are switched on in the Scenery Library even though they may be installed still within FSX?
Yes, of course. The cache regeneration is never total, it only regenerates what has been changed from the last run.