Yeah, welcome Neil :D
I'm quite surprised as well - the Apaches are the "fattest" ones I've come across when compared to other strat pups. I've got Irish Tours, Sultans, and Apaches. The differences when putting them in the same guitar are noticable but not huge. The Apaches definitely feel rounder, smoother, and possibly more "meaty", to me than the other two do.
Comparing any of them to my other guitars, though (Riff Raff, Mule, MQ, even Blackguards to some extent), all strat single coil pups I've tried sound a bit thin and possibly overly gritty when overdriven - I adjust the amp if I want a strat kicking out the same sort of tone as the humbucker guitar I was just playing. BUT(!) I suspect you already know this anyway :D
One thing I have found out with the Apaches, and this is just experience of two guitars, they do seem to pretty much amplify the tone of the guitar itself. The job they did in the first guitar, while similar, is not exactly what they do in the second. Personally, I've found this more noticable with Apaches. So it could be it's just not a good match in your guitar.
Height-wise, mine are set roughly 2-3 mm from the high E when fretted at the last fret (bass side slightly lower). I have tried them lower than that and, like any pickup I've tried, they thin out a bit then (or get clearer, depending on what you're after!).
I've got a feeling I'd contact BKP over this one. I've read about all sorts of reasons for people not getting on with a specific pickup in a specific guitar, but I don't ever recall reading about Apaches being "too thin for me" in comparison to other strat singles.
Good luck :D