So, I will preface this with the fact that these issues seemed to resolve upon restart and I did grab a copy of the log file (not sure if it was too late, though), but I was experiencing two bugs - the cabin scene (just after Alex has a panic attack), and the first meeting in Mayhew's tower.
For the cabin - despite multiple attempts - keeping it serious with Nick and Connor, turning off that one little setting that would indicate a certain interest, etc., and selecting a majority of the vampire influence settings (playing as wary but open minded, still getting vampire influence specific dialogue it would seem) - Alex was always greeted by Connor when he wakes up. Since this was a file where I want to try and romance Mayhew, the aim is to have Seth there when Alex wakes up instead. I was planning to keep trying different combinations, but I remembered the old 'turn it on and off again' method to fix things and that did resolve them.
The second one, I only noticed because of the first (I realised it was an additional oddity in all the skipping). Although I was selecting the options of 'I'll help you with this, but I can't promise more than that', and, 'I may in time' (in response to Mayhew asking if Alex trusts him), Mayhew told Alex to go home - and Alex woke up at the tower the next morning with Paolo instead of at his flat with Maxine.
Again, these issues did resolve when I restarted the game, so I'm assuming the issue was local/session based rather than a general issue in the code, but it couldn't hurt to be informative.