I went to the main booking hall at St Pancras and explained the situation and asked whether i could get anything back for my unused ticket. I was told no and so purchased a single ticket for £58.50.
So it looks like i might have a very slim chance with EMT in getting some money back and perhaps my fare back from TFL.
Next time, I'd do one of the following:
1) Use Oyster PAYG from Upminster (not LU Upminster Bridge) on c2c, ensuring that I touched in with plenty of time to spare before the last valid connection for the through journey,
or
2) If I had to travel from Upminster Bridge, I would purchase an Advance from
Zone U1256 Londn
In either of these cases you'd be covered!
However, what I'd have done when the ticket office refused to apply discretion, would be to thank them and not cause a scene, but simply walk away and go to the gateline (perhaps not directly if it was in view of the ticket office). I'd then approach the Guard and explain the situation. Many Guards would apply discretion. If they do not, the charge is exactly the same on board in these particular circumstances - so you'd have nothing to lose.
Most Train Companies won't be so pernickety about using Oyster PAYG to start your journey on LU (starting on LU is fine on a paper ticket; starting on PAYG is fine if using National Rail, but not the two together :roll

, but EMT clearly are, so the other alternative is to avoid EMT
- it can be both quicker and/or cheaper to use East Coast, and even if not, you'll be more likely to be treated as a valued customer.
By the way it's not entirely clear what your planned itinerary was, nor what train(s) were delayed. If it was, in fact, a c2c train that was delayed, or your journey included travel on c2c, you might actually have a claim.
While we know that an LU journey starting on Oyster PAYG isn't covered, while starting your journey on National Rail (but then optionally using LU) is covered, it's not clear what the situation would be if your journey was LU > National Rail > LU > National Rail, which I'm guessing it might have been, if you were changing at Barking?
Of course, I agree with thedbdiboy's interpretation if you were using c2c for part of your journey, but sadly the documentation isn't quite up to scratch, so EMT might take a different view.
I am happy to proof read any letter of appeal, but I'd want to know more about your exact planned itinerary first!
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Were you at Barking station by
1120? (or at Upminster station by 1112?) If you were, I believe you have a valid claim.
If you were not, but set off from Upminster Bridge in good time to be at either Barking by 1120 or Upminster by 1112, then I'd also say you
should have a valid claim but that will be very much open to interpretation.