Not being into the .40S&W, I am unaware, ARE there crimped primer cases in .40S&W??
My understanding has always been that only military cases had crimped in primers, and, as far as I know, the .40S&W isn't a military cartridge. Which doesn't mean its impossible, people do weird stuff, like small primer 45ACP cases...
Over the years I have noticed that some primer brands are just easier to seat than others in general. Remington primers (back when they existed...) were always easier to seat than CCI.
One possibility is the shoulder (edge) of the primer pocket being too "square" to allow the primer to slip in easily. Another is primer pockets at min spec and primers at max spec.
Trying a different combination of primer and brass is the old solution, but that was back when you could find a variety of both on the shelf at the store.
If the entire primer pocket is too small, then a swager type tool is needed. If its just the edge of the pocket, then a twist with a chamfering tool will break that sharp edge and might just solve your problems.
Might also call Federal, tell them your problem and give them the Lot# of the primers you're using. Might be a bad (very slightly out of size spec) batch that they know about. Might be news to them. No one can fix a problem they don't know about.
First thing I'd try would be sticking the nose of my deburring tool into the pocket and giving a twist. Won't take much. Then see if that makes a difference in getting primers seated. If that solves things, you're golden. IF not, more investigation is needed.