Any chance the sizing die or shell holder is deforming the rim? Could you chamber the brass again before resizing? If you can rechamber the fired case after firing but not after resizing I think your die or shell holder are to blame.

When I annealed my cases after forming them to 35 caliber I worked real hard not to anneal the shoulder. On a Krag annealing the shoulder is not so dangerous as on a bottle neck cartridge, but personally I do not think it is good practice.