Last year I experienced issues loading once fired 5.56 brass on my Dillon 550B.   I used a RCBS swager to remove the crimps but 50% of the premiers were difficult to seat. I'm reloading again so I bought a Sinclair reamer to clean up the pockets, this helped but still I have 10% or so that are difficult or won't seat at all.  This is a problem on a progressive press as it screws up your sequence fixing the problems.  I reload 2,000 round at a time and clearing jams has doubled the normal amount of time.  Also, I ran out of 4895 and all I could find locally was Vargent and Reloaded 15.  25 Grains of Vargent nearly fills the brass and makes a mess, I'll give the Reloaded 15 a try tomorrow.  Why are the primers so difficult to install?  I'm using mostly range brass

I'd recommend the Dillon swager. Because I KNOW it's good and gives very consistent pockets and primer seating feel in the press.

You might want to take the time to sort your brass by headstamp.  Brand at least.  That can only help with consistency.

I use Hodgdon H322 powder which comes up to the base of the case neck for the loads I use.    Interestingly enough I use the same charge (21.5 grains if I remember correctly but don't use that without checking the load data) for both 53 and 77 grain SMKs. This is OK per the loading data.

I use an XL650 press.  Yes, I know quite well how a bad operation messes up the workflow.

I use a Dillon swager and have zero issues seating primers when the swager is properly adjusted for the worst brass in the bunch.

Either that, or pre-sort by headstamp before you start swaging.  Different brands of brass has different case web thickness, and results in different levels of swaging.

I was thinking of not priming with my 550B using my Lee handheld priming tool or my Rockchucker press instead. Good to know about the Dillon swagger, I’ll probably end up with one.

I also prefer to hand prime or use a Lyman Ram Prime on a single stage because I can "feel" how well the primer is seating.

I de-prime, clean, and then size all in separate operations. I swage before sizing.  When my brass hits the progressive to load, if I have a primer that won't seat, I pull it out and either ream it or replace it.  It doesn't disrupt the operation very much.

I will say that this happens much more with 9mm than with .223.

The swager can only be set for one brand of brass at a time.  They tend to differ between brands.  I have my swager set to where it works on most cases.  You can also set your swager too deep and primers fall out.

I use the Dillon Super Swager also and have found that if I set it to swage out the crimps of LC military brass to where I can smoothly seat CCI 41 primers, all other brass swages out nicely with factory brass untouched. I clean, size/deprime and swage separately and then load on my Dillon 550 with no issues.

Bird

I ended up getting a RCBS trim station with a military crimp cutter.  Works good, no more problems installing the primers.  One thing I did notice was sometimes the primer would go in with no resistance in fact several primers fell completely out when I put them in a bucket.  Later at the range I had a stoppage when a primer jammed my trigger!  These loose primers amount to about 5% of the R A 6 5 (Remington Arms 1965) stamped brass that I have.  It took me a while to figure out WTF was going on.  Have any of you experienced loose primer pockets in military brass?

Where did the RA 65 brass come from ammo you fired?  Brass you picked up at the range?

Brass changes with age, some exposure to certain chemicals (ie ammonia) can weaken the brass.  Scrounging brass at the range is another source of issues.  
Unless you watched the guy take new ammo and fire it.  It is hard to ascertain how many times brass has been fired.  Rifle brass heritage is important.  
Brass you might scrounge at the sets you up for issues as you have no idea how many times the brass has been fired.

I acquired this brass in the 70’s.  It was all tracer but being so old the tracer feature was unreliable.  I used it as training ammo on wet days so I didn’t burn the woods down.  I had hundreds of boxes (3-4,000 rounds) of this and still have some left.  I saved and processed the brass.  A small percentage of it has the large pockets and now that I have it figured out it’s less of an issue.  This is training ammo only.  My go-to-war ammo is kept separate.

I gave up on press priming yrs ago, as you said, 1 problem really grinds things to a halt.