John the major problem with the Encore is in the action. There is a gap between the back of the barrel and the face of the frame. The easiest way to see this is to take a feeler gauge and close the feeler gauge up in the action. Most Encore's have .002 to .004 gap. Just start at the .001 gauge and close the action, you will be able to pull the gauge out. Just keep going up .001 at a time until the gauge will not pull out. That will tell you how much gap your particular rifle has.
Now to the issue. When the firing pin strikes the primer it pushes the case forward(because their is nothing to hold the shell). This is one of the reasons for some shooters who get misfires. The primer is still struck, but when the shell is pushed forward there is not enough energy to set off the primer. That is why I like a rimmed cartridge. The rimmed cartridge can not be pushed forward. Therefore you get even-constant ignition. The fellow at EABCO explains this very well. As well as Mike Bellm on his web site.
Now your sizing problem is occurring when the shell is being pushed forward(because the 30-06 headspaces on the shoulder) to the shoulder, then it fires. the casing is then expanding to the size of the chamber, plus the size of the gap in your particular rifle. Just measure the length of your brass before it is fired(new brass), against the length of the brass after it is fired one time. You will see the difference.
It is not recommended to shoot brass from an Encore in a bolt action after you fired it in the Encore. You are working the brass too much. There is a better way to size your brass for the Encore. There is a great article on the Mike Bellm site giving step by step instructions. But for this conversation lets just say that it is a different way than how you size for a bolt.
It is not difficult. It is just different. Once you get the hang of it, it will come easy. But just to suffice to say that you can not effectively shoot the same brass from an Encore to a bolt-or any other rifle for that matter.
For most reloaders they just size their brass the same way they have for all their other rifles. And it will work that way. However it is not the way to get the best accuracy out of your rifle. When you size your brass properly for an Encore you will see an increase in accuracy(or at least we have). A lot of people are disappointed in the accuracy they achieve from their Encore. And IMO alot of that can be attributed to how they size their brass. Most relaoders who have accurate rifles only neck size their brass for ultimate accuracy. And unfortunately for the Encore it is not the best way to get the best accuracy.
Go to the Mike Bellm site and read his articles about sizing brass, and headspace in the Encore. You will be glad you did. Tom.