My iPhone 4 is also about 60 sec boot up after 1.5. That's typical for a 4 and no indication of any trouble. iPhone 4 is just a slower machine than 4S or 5. Boot up of stock ip4 is about 50 sec too. So we only lose 10sec after jailbreak.
You guys are right !!! My Bad !!! I just restored afresh(without JB) on 6.1.2 & same issue with Bootup as well as Home Screen time-out. Never happened on 5.1 or 6.0 though, so i guess it's 6.1 that's causing this.
Time to get a new phone.