I have the latest 3.1 with winterboard and initially I was getting the same symptom "Safe Mode" activated. I restored again and then loaded one Cydia app at at time to try to isolate which one was the menace. Load the primary packages first. Then the nice to have stuff. The bad app for me was the Glasklart Live Clock of which I believe there might be other Live Clock apps out there causing the same prob. It's been about a week now and no safe mode issues. Got the latest Cydia updates which I presume may have helped, i.e, mobilesubstrate and what not. It's all a hit and miss when you make an upgrade early on. The Cydia apps writers have to play catch-up to stabilize and verify that their apps are stable on the new OS (This takes Time!). So for us early OS adopters and jailbreakers...it comes with the turf!