Check you primers on a piece of glass. If it rocks at all the primer is too high. After a while you will develop a rhythm with your reloading and get a "FEEL" for your primer height.
BEWARE, if you just set the depth too deep you can crush the anvil and all you will be making is duds!!
One other thing that can cause these problems is CARTRIDGE OAL length as well as just CASE length. Check BOTH, its more likely its case then OAL as generally the handy will not even close if the cartridge OAL is too long. But brass is very elastic and will compress and rebound causing the problem you are having.
As far as sizing, you need to re-read your reloading manuals. Just brush up on die setup's. You shouldn't be moving the shoulder at all, assuming these are YOUR fired brass. I keep range brass, (Other peoples stuff) separate from brass fired in my guns for just this purpose. Also most of my guns are neck sized only, this necessitates the separation.
I like to clean, re-size, clean again then trim, chamfer, and prime, then charge with powder and bullet. I load my rifle stuff single stage for the most part. I used progressive for the semi autos when I had them, now I only load pistol/shotgun stuff progressive.
Redding dies are top shelf, Lee's are cheaper. But I would say its unlikely the dies are your problem. Both are up to the quality of any hobby re loader, no question. Possibly their set up...... You mention "some hick-ups" with the 25-06 in the handi...why? What are the problems?
Good luck,
CW