From my own personal experience... The thinner head is likely causing the tom to resonate more than before. Also, one of your tom heads may be tuned to a similar or sympathetic frequency to the snare, causing it to excite the snare more than before.
Fixes: Retune the tom (one of both heads), retune the snare (one or both heads) or move the tom away from the snare a tad, and see if that helps. Also note that the size of the room you play in REALLY has an impact on how much one drum excites another. A small room will usually make the drums excite the crap out of each other. In a larger room, the sound waves coming from the drums have somewhere to go and/or dissipate, so they excite the other drums less.
This is a real problem with Kent drums likely due to the very thin, resonant shells. I'm about to re-head a Kent kit (20", 12" 14") with thin heads and I may end up regretting it - LOL!!! I really want that open, higher-than-rock jazz sound.
I have another Kent kit in the larger 22", 13", 16" sizes and I ended up using Aquarian Studio X heads on top and Evans clears on the bottom. Even with the Studio X's thin muffle ring, they still ring out like a bell. Had to be very careful when tuning them up so as not to make the snare go batty.
Whatever you do, don't start slapping duct tape on the bottom of the snare head (across the snare wires) as I've seen suggested elsewhere.
Good luck and let us know if you solve the problem.