Problem fixed. The restart wasn't a full restart - as such, the database cleanup routine did not run correctly. All vehicles that were in the game-world prior to 4pm were still marked in the DB as 'active', hence they were not available to garages - but they did still exist.
We performed a second restart at 5pm, and all of these 'limbo' vehicles were then properly marked as 'back in garage', and became available again.
Sorry for the inconvenience; new server, new batchfiles, still some tweaking to do, evidently! Future restarts will be full shutdowns to prevent this happening (we basically wanted to see if a 'warm restart' worked, because they are quicker, but clearly they don't!)