Hm. Well, running cv's VideoCapture will change the v4l2 type used for data acquisition most likely to one of the non-radiometric formats, which will disable t-linear radiometric in the firmware. It should be when re-selecting the Y16 format, the firmware is supposed to re-enable t-linear radiometric on those parts, but maybe that's not working for some reason.
The reason the spot meter would work but the data would be wrong is simply that the spot meter reads its value out-of-band using the Lepton CCI interface (and not the data stream).