With my own writing I've found the order of the Variations in the PSR definitely doesn't line up with the SRCA (1234) order in the story. Yet, I've found the PSR Variations to be incredibly accurate, to the point of being spooky!
One thing to point @lakis, the PSR is like Dramatica's version of a hash function -- it's very sensitive to the smallest change in the storyform, at least in my experience. (Except for Story Limit, that usually doesn't seem to impact it.) So, if you find the PSR doesn't seem to line up with your ideas, it might be that your storyform could need a bit of tweaking to match your subconscious ideas.
On the other hand, I've recently been wondering whether a writer's subconscious might sometimes vacillate between 2-3 close storyforms*, not cementing things until after finishing the first draft. (Especially if you don't outline in much detail.) If that's true, using the PSR might be one way of getting your subconscious to settle on a single storyform!
* This has been happening to me a bit on my current project, which I decided to outline in a lot less detail than my last one. I'm well into first draft and I've got most things worked out, but sometimes wonder if Problem and Symptom might be flipped ... and I'm really not sure on the Judgment!