After checking with some of the experts, examples where manual inputting will be required are:
flights on routes which go through active Danger Areas,
flights which are being rerouted on to tactical CDRs when a Danger Area has been cancelled earlier than scheduled,
flights which are on infrequent routes which have not been 'adapted' in the Flight Data software (if the plan is accepted as filed, the controllers will get all sorts of wierd and wonderful strips from the system since it is using direct route processing and not a controlled adaptation),
flights which have filed point to point routes in the Upper Air Space (this is not allowed in UK AIP, but IFPS will still accept them if the maximum distance between DCT waypoints is not exceeded),
non standard flights,
etc.
This is not an exhaustive list and some of the problems most definitely lie with the UK Flight Data Processing system, however, the contingency for this is the minimum filing time which is supposed to be followed
There are obviously a few disconnects between what IFPS can accept and what the UK actually wants. Some are being addressed with fixes (Danger Area and CDR conflictions for example) and some are probably in the too difficult bucket given the UKs differing types of airspace (DCT route problems in certain classes of airspace).