Assuming you've gone through adjusting it correctly/differently, cleaning rims, brake pads, and they've bedded in etc, etc.... it could be the new wheels in combination with the frame, etc, now cause the squeal (new natural frequency of oscillation?). I went through something similar -drove me crazy -and eventually cured it by using one of those old fashioned brake boosters (cheap off
ebay, but obviously you have to have cantis/v-brakes and I'm not sure what kind of brakes your hybrid has)..
You could also try different brakes (even of the same design) or pads too (especially if you have some spares hanging around to see if it makes a difference). If you have mudguards try removing them, or if you don't have them, adding them. Or go back to the original wheels.... Or just accept the squeal. I tried brake boosters because they were the cheapest of the options and did the job for me.
Hope you get a cure.
I have just fitted my new FSA wheels to the hybrid after cleaning the braking surfaces with brake cleaner and went on a little test ride, the horrendous brake squeal was too unbearable so came home, cleaned the rims and pads again with a brake cleaner but has made no difference, the pads are 105's and were fine on the original rims.......any advice please?