In the Job Queue, there were quite few of these messages.
Looking in the vlog, it seems that this file was deleted earlier on in the day. This explains why there was an error in this scenario.
05/02/2014 07:00:36 Files have been deleted from the vault.
User:XXX; Vault name:<Vault>; Vault filestore root:'D:\Autodesk\ADSKVaultFS\<Vault>'
Vault file:'$/Trash/5521378.ipt'; Relative filestore location:'000\000\000\000\001\075\1075868'
Note: File deletions are not enabled by default. These must be enabled in the web.config (see "Tracking Deleted Files")