I have encountered this problem consistently over the past several years, and after researching, theorizing, and experimenting, have formed the following conclusion:
Dead spots aren't just a matter of neck density but also of stiffness, right? Well, by changing the string type
you have effectively changed the neck's stiffness a considerable enough degree to affect it's resonant frequency, thus also affecting the dead spot. Please note: tension
the same as stiffness
. A set of Balanced XL's and a set of matched (Balanced) Chromes will have the same, or incredibly close, tension, but vastly different stiffness. That's what I'm talking about. I have found going from rounds to flats or vice-versa to be the biggest perpetrator of this phenomenon, not so much gauge, which wasn't very apparent unless it was a drastic difference, i.e., 40-95 to 50-115 at the same tuning.
Hope this helps, and as always, acronyms: IME, IMO, SOS, DMV, YYZ