Ello mate!
That is odd, agreed. I'd have automatically said it's a feature of the processing setup that's making it more difficult to get harmonic feedback..but as you mention that it happens with your amp, it's obviously something else.
Sounds ("gut reaction" here) like it's a combination of a few elements here:
Firstly, is the amp a valvy or SS? (Feedback a little more easy with the former)
Secondly, sounds like the pickups have had the effect of accenting some frequencies whilst effectively dampening others...another way of looking at this, is that perhaps with your former pups the type/method of winding allowed some frequencies to dominate the sound. The BKPs may well have restored a balance that you might not have anticipated. Now, I know jack about pup mechanics, so I'll shut up before I go down a road I've not travelled!
The tone control thing is not a coincidence...my capacitors do not quite have the same effect as before my BKP upgrade.
Maybe I could be more helpful by suggesting that the present pups are at least freer of nasty microphonic-style feedback..? Tell you the truth, I too have to work a bit harder to get my "old" sound...the trade off being that my Mules now give me a different one. Don't get me wrong, I'm not a BKP fanboy but I do know a good product; mind you I must also throw into the arena that my guitar is presently in hospital to sort out a high-frequency hum that was not there before...maybe there's all sorts of aracana at work in the winding/matching of the bucker coils of which I'm unaware.
Don't worry, you're not going nuts by the way!
If I can finish on a more helpful note, have you tried just putting a wah between your axe and the amp, ensuring you ramp up the pre-gain on your amp..? c--king the wah at "wolf-frequency" points really does work well with BKPs to lift and feedback certain notes..actually more pleasingly than my stock pups...my closest example that I've yet put up in "Players" is my first Yammy one: this has something like wot I'm trying to say!
Best of!