So, this service was 30-down by the time it got to Grange over Sands (which is kind of impressive in a depressing way). It's now not stopping at three of it's planned station calls in a vain attempt to make up time, but will still likely be 20+ late on its return journey.
What a very Northern way to introduce a new train.
It would be interesting to know what the problem was, since it doesn't look to have lost any further time (to speak of) after Grange. It actually left Manchester Airport a few more minutes down than it arrived, so it looks as though there was still some issue to sort out.
As to missed calls, the three it missed southbound were the three it should have called at after Piccadilly - Burnage, Gatley, and Heald Green. (RTT says it actually called at Heald Green, but it also gives identical arrival and departure times, so I think we can conclude that it didn't.
On the return it again skipped the stations it should have called at between the Airport and Piccadilly - Heald Green and East Didsbury.
Being 27L southbound at Picc makes me wonder why it wasn't terminated there, but it's likely there were considerations I don't know about, and I'd be the first to say that this terminating prior to a booked destination does go a shade too far sometimes.
I have to say, I've never known a train be diverted from its booked route without good reason. Okay, sometimes that reason isn't immediately apparent, but investigation usually finds it.
I've looked back over the past week and found that 1Y91 operated via its booked route Monday/Tuesday/Thursday - on Wednesday & Friday it didn't operate. As you say, its operation is anything but guaranteed at the moment, and I would say that Barrow duties are every bit at risk as duties worked from Greater Manchester/Merseyside bases. I can't help but think that this 'new' service is, as has happened so many times before, going to be blighted by unreliability.
I see that the 1147 ex-Barrow is being terminated at Preston, and the return 1429 Airport-Windermere is being started there. I don't know what time these facts were announced, but it was long before the train was due to leave Barrow. So it doesn't look as though the service is getting any sort of priority, first day or not.