I've found that bottom bracket creaking usually comes from crank bolts not being tight enough. Since you've just reinstalled the cranks, make sure the bolts are tightened. With tapered bb axle, you need to retighten the bolts a couple of times in the first 100 km.
If that doesn't do it, try overhauling the headset. The creaking might be coming from there. A good test is riding the bike no-hands. If it's unstable (feels like it wants to fall), you've probably got rust in the lower hs bearings. You can't tell just by lifting the front and swinging the bars back and forth.
I ride a fixed gear year-round and addressed the same problem as above.
- L.