It also appears that on SS3 SD4.6 works slow, and not as smooth, I got some force closes as well. Could that really happen due to SS3? Coz, while on SS2.1 SD4.6 was rock stable and very smooth. For now I have reverted to SS2.1. I will wait until SS3 is a little more stable.
EDIT: After flashing SS3 again, and doing a clean wipe several times (after flashing the ROM on slot 1) and letting it settle for a couple of days, SD4.6 seems to be working fine again. Also, I posted link to how to get into SS3, if you are having issues with it.