So, are the stylesheet files themselves missing, or are they empty?
In either case, I'm not sure yet what can be done - although a check was suggested, it's not really a fix. But it doesn't seem like something that can be easily controlled because it seems to happen randomly. It's possible that the file can't be created / updated because a user is requesting that file. If you disable the wiki before saving (vBulletin Options > VaultWiki: Server Settings > Enable the wiki) do the styles all propagate correctly?
Are you dangerously close to your server's disk space usage quota? Is there a quota for the /clientscript/vbulletin_css/ folder?
When the file IS created successfully, what is the file size of the sometimes problematic files?