neilmac: To be fair, nothing that's happened to you is the fault of JPA. The same situation would have occurred before because it's the allowances that are the problem not the system delivering them. (But £100 sounds very low, you should be able to claim unacompanied baggage + 1 private car rate for the move - I think....)
With regard to the HR people not cancelling your flat, you will have put it in writing to them so there will be an audit trail and you can claim the arrears back! Sorted!