Did you use same number of bearings as were in the retainer? If so, could be that the clicking is bearings bouncing around because without retainer, there is more space in the cup. Add a bearing or two to take up additional space made available by removing the retainer. Or put the bearing back in the retainer.
Don't bother with the retainer. Re-pack it loose, (full - 1) amount of bearings. Spin the cranks without the chain attached. Consider that the clicking noise can be coming from say the pedals. The condition of the bb cups will be apparent with a ballpoint pen trace. Make sure the cranks are attached with the proper torque.