I am experiencing some issues with resizing the shoulder on my brass.  

When I load the brass into my chamber, the shoulder is hitting the front of the chamber causing it to be difficult to close the bolt.  most of them I had to bang the bolt close with my hand.

I know this because I sized some brass and then painted them black with a sharpie before trying to chamber the unloaded brass.

All the brass were the same, they had circular scratches in the marker indicating they are rubbing on the inside of the chamber. scratches are on the shoulder of brass only.

The rifle is a Serbu 50 single shot.  The size dies are Lee master set.

The size die is set as low as it can possible go in relationship to the shell holder, it is sizing the entire brass.  

Any ideas?

You really need some sort of chamber sizing gauge to be sure you are sized to spec.

Do you feel the press cam over center when operating it without a casing in it?
Generally you should feel some resistance, not just make the die touch the shell holder.

Where in PA are you located?  PM me if you don't want to post it.

Did you trim the brass?

Does factory/other ammo chamber OK?

I use custom Lee dies to load 510DTC.
I was having the same problem intermittently.   I had two shell holders and found a variance of about .003" between the two.  The shorter one would size perfectly but the other would not.  

I turned the shell holder in my drill press and used a file and emery cloth to remove  material from the top of the shell holder and it's perfect now.  You can experiment by using a feeler gauge to space under the shell to space it up towards the die.

I have resized well over a couple thousand cases and have found that putting the brass in the sizer will not guarantee that it is sized. With all the brass that makes up the 50BMG it tends to spring back a little causing these problems. What I do now is resize the same piece of brass 3 times. Meaning when I pull the handle and size it for the fist time and the brass is up in the die I kind of just bounce the handle with some weight a little then I pull it far enough so about 50% of the brass is out of the die and twist it with my fingers about a 1/3 of a turn and then put it up into the die again. I repeat this one more time and by the last time it goes into the die easier and have not had any problems with it fitting in any of my rifles since. This works on all brass but is a must for mil surplus MA Deuce brass.

BTW I learned this after loading about 400 of them. I did test fire a couple before loading up the 400 API but because I did it in my M82 the inertia tended to let them seat far enough to fire. After trying to put them in my bolt rifle I was having the same problem as you were. Instead of removing 400 bullets and powder my fix was to mill off the top of a full length sizing die and have the loaded round shoulders bumped back in the sizing die as the bullet and most of the neck come through the top. This worked and I have since fired most of those rounds without any problems.

Another BTW I don't buy any more brass that has gone through the MA Deuce as it is a pain to resize and I don't get as many loadings out of them.

Problem solved....  Brass slides in like butter now.

Not wanting to alter my dies, I decided to shaved the shell plate down a few thousands,  I flat filed the top of the shell plate, Re- set the die and presto chango just like it is supposed to be.  Chamber shows no indication of rubbing shoulder area now.

I did this slowly, i sized a brass, painted the shoulder, chambered the brass to see signs of rub.  I then shaved the holder some and repeated until I no longer had scraps in the marker on the shoulder.  

Thanks for all the input.

I think you new reloaders need to learn to anneal your brass on the necks and the shoulders to permit proper re-sizing. Please don't take this as an insult to your abilities. The 50BMG case has so much more brass in it that it retains a memory especially after work-hardening which occurs naturally on every firing. Annealing every time to every third time will allow for better control of your sizing operations.
I too size 3X rotating the case in the die about 120 degrees each time, I find it helps with concentricity. Being able to present the projectile correctly into the bore will help your accuracy potential. As we all know, it is the loose nut behind the gun that makes or breaks that accuracy potential...
Cutting a shell holder is a fix, and better than cutting the die which some have done. Another fix is trying a different lube which may have a different sizing pressure characteristic. Some use Imperial sizing wax which is very good, but I now use spray lanolin which I make for my own use. Dillon lube, Hornady One-Shot, and other spray lubes work also, and this application of lube prevents over-lubing which can cause shoulder dents.
Ask if you have other questions.

I also resize twice but I like the idea of thrice sizing and rotating. My problem is that whether rifle fired or Ma Duece fired brass I can fire 10 rounds and have 3 or 4 stick tight enough that I need to tap on the bolt. The other 6 or 7 don't require any force to lift the bolt. It drives me crazy . No matter what charge I use the same thing happens. Any comments?

Oldman has a point and probably knows more about 50s then we ever will.  Check into annealing your brass and it will stop it from springing back.

All brass was annealed prior to resizing, primer pockets uniformed, flash holes deburred, trimmed on Giraud trimmer, etc.

Plus you need a good case lube. I roll my cases on a lube pad with Dillon Spray lube applied. You need to get enough lube on the outside neck and a nylon brush to apply lube to the inside of the neck. I have much better results by first punching out the fired primer in once fired military brass with crimped primer pockets. Make sure your expander button does not bottom out on the inside of the case. My sizing die has to be adjusted close to the bottom to punch out crimped in primers. Firm contact with the die and shellholder is usually necessary and with cam over. Removing material from the shellholder in your case evidently worked.

I make a de-priming Punch for removal of primers prior to any other operation.

PM me if interested.

Use with a shell-holder and a brass hammer.

Buy one, it'll save a lot of headaches:
http://www.lewilson.com/casegage.html

I have case gauges for all the calibers that I reload reasonable quantities of. I.e..223,  .243,.308, 7mm Magnum, .375 H&H and of course 50 BMG.

the only reloads I don't gauge are the ones I don't have gauges for (which aren't many)
I really like the "slotted" gauges.