From previous phone call discussions with Calmini as well as those here with the lift, yes, the forward upper housing mounts are overall taller in respect to the stock mounts. The pinion mount stays as stock, so yes, basically you are binding the pinion mount as the longer mounts drop/rotate the housing. Drop/rotation should be near 3/4".
If you want, compare your diff housing to mine in my pics. This should tell you the 'rotation' you have with the brackets installed. Too bad you didn't snap a shot comparing the stock mount to the Calmini mount.
As for the rubbing under certain front conditions, try removing the front ds from the pinion and secure it to the crossmember. Lock in the hubs (got lockouts?) and drive. The tires rotates, the axles rotate. If the binding occurs, it's tires input to the shafts. If not, reattach the front ds, un-lock the hubs, and drive. The ds will rotate the axle shafts. If binding occurs, it's driveline influenced and could be the pinion mount and not the shafts.
To add, does the pinion flange have bright spots from rubbing on the crossmember?