I took some time to investigate this; the TL;DR is that Husky works perfectly well against HW crypto.
(As an aside, all of our most recently introduced FPGA target notebooks – 6 by my count – have been developed using Husky.)
My results on the sca201/Lab 2_2 notebook, using 15k traces:
CW-Lite: 15 out of 16 key bytes recovered
CW-Husky: 14 out of 16 key bytes recovered
YMMV but these are not cherry-picked results.
I used samples 700-705 for the attack with CW-Lite.
With Husky, I shifted the window to 703-708 because Husky’s sampling latency is 3 samples less (as documented here).
With CW-Lite, I used the default setup, with sampling set to clkgen_x4.
With CW-Husky, I used scope.clock.adc_mul = 4 (for fairness) and found better results with scope.clock.adc_phase = 131.
I did come across this issue when playing with adc_mul and adc_phase; this may have been the cause of your poor results above.
To conclude, it’s simply luck that the Lite’s default settings give better results than Husky’s default settings. With a different target you may well find the opposite.