Kar 98 Mauser action - bolt won't close on round

I have a rebuilt Kar 98 .30-06 bolt action that will occasionally fail to fully seat a round, the bolt won't slide all the way forward, preventing the bolt handle from closing. Has anyone else ever had this happen or know why this would happen? The action is WWII era, but was re-fitted into a different stock for hunting in the 50's or 60's. It was given to me by my grandfather and I would love to continue to shoot it and hunt with it.