The issue in significant part comes from the way in which PPM is measured, and then managed by operators.
When initially set, it expects that there will, inevitably, be a proportion of causes of delay in running a public service. The measure is set, in significant part, to encourage operators to put all endeavours into getting a disrupted service back to normal again. So if, to take an extreme example, an aeroplane crashes onto the railway, there is an encouragement to minimise the disruption rather than say for the rest of the week "oh well, not my problem ...". The same applies to minor disruptions, there is a PPM allowance but not much beyond, so you should have to try.
HOWEVER, what has happened is that operators have increasingly seen the PPM allowance as "theirs" only, and will actually plan down to the allowance for their own internal issues and minimising costs. Short staffed for the weekend? Well, if we have a (for example) PPM allowance of 90% for delays and 95% for outright cancellations, as long as we come in within the 95%, that's fine, and we can cheesepare our staff numbers down to achieve that figure. Then something else happens and it's all disruption. But never mind. We put up loads of posters threatening prosecution if passengers don't buy the right ticket in advance, before they even get to the platform, and most don't claim delay repay anyway, so on we go.
I see GTR have now told platform staff they must not load PRM passengers by ramps if this will impact the punctuality of the service
http://www.bbc.co.uk/news/business-44172072 . I couldn't quite believe this when I heard it (but GTR confirms it - see link), and feel it may well contravene the Equality legislation. But this is just typical. The PPM allowance anticipates such issues, and the operator should allow adequate turnround allowances and crew scheduling to handle minor issues like this, but the operator has taken all the allowance for their own internal delay-causing economies, with minimal turnrounds at both ends for hours, crews scheduled right up to the minute, etc.