I've previously looked into GPhC pass rates, and I think it's normal for them to drop between July and September; the latter month tends to have a higher proportion of first sits, so you would expect to see a higher pass rate. While 95% - 40% is a rather jarring drop, I believe it follows the general trend.
As to why September sittings are lower than July? Dunno. But I will say this: The pre-reg exam is a very different beast to Pharmacy exams, in that you can't get through it on a wing and a prayer. It's not like sitting down and writing an essay on the metabolism of Paracetamol, where you can scrape enough marks through piecing together the few bits of the course you remember (alongside some other waffle), when you're faced with a multiple choice question on the contraindications of Paracetamol, you either have that specific piece of information stored in your brain or you don't. There is no room to really blag, only to make half-educated stabs at the questions. End of the day, you don't work your ass off to revise for that thing, you probably won't pass - first, second, or third sit.
That said, I personally found the pre-reg exam I took to be a little on the unfair side. We were questioned about things excluded from the syllabus in the closed book and asked about material brazenly outside of our reference sources for the open; while good exam technique meant my answer to these questions was simply putting 'C' and moving on, I can imagine how someone might have been seriously thrown by these questions popping out of nowhere.