The library specific thumbnail cache must be exactly in sync with the database files. You can use a single thumbnail location and a single library location for several MC instances only if you never run more than one MC instance at a time.
What, never?? ? I was under the impression that you could have two copies of MC open and accessing the same library, but that only the first MC that was opened would have write access to the library. Is that wrong? Could the simple act of opening MC on both machines corrupt the database in some way?
In general I would recommend saving the captured images to disk files (Screen Grab to File) and linking those files as video cover art. Then the thumbnail source would be a jpg file and if you ever need to recreate the thumbnails it will be easy and fast. You would also be able to have a single library location, two separate thumbnail locations, and see the captured images on both MC instances.
I think this is probably the way to go. I've tried capturing the thumbnail as normal, then 'Save Cover Art To External Location Specified In Options' (which points to another NAS folder), in the hope that I can add cover art quickly from that folder when it messes up again.
In addition I would recommend keeping the thumbnail caches on fast local drives (you will probably need to use two separate locations anyway). The thumbnail files can be quite big and MC accesses them constantly when the library views are browsed. You may be unnecessarily sacrificing some of the browsing speed when the thumbnails are read through LAN.
I know what you're saying, but speed isn't much of an issue to me at the moment - plus I find it's pretty quick running over a Gigabit network. If I ever get this working the way I want, I might go down the route of setting up an elaborate sync mechanism to do this, but right now it's not a priority for me.