I recently reloaded  a bunch of AR-15 ammo, I used IMR-4064 with a Sierra 55gr SPBT boat bullet, I used the 5.56 dies. The first shell out of the clip jams. When I use a factory load first and then the reloads to follow they cycle fine? Why wont the reloads cycle first out of the clip???

The first shell out of the clip jams. ...Why wont the reloads cycle first out of the clip???

You're supposed to remove the clip and spoon from the magazine before loading it into the rifle.

Ok, so seriously, need better description of the nature of the "jam." Pictures help.

^ This.  Is that first handloaded round not chambering at all or is it not ejecting after firing?

Begin with the rifle bolt down on an empty chamber and no magazine in place.   Load the full magazine into the magwell and hit it on the bottom to lock it in place.  Then rack the bold back and release.   Does it chamber the round, or is it failing to strip it from the magazine?  If it strips it from the magazine, does it chamber, or is the bolt only partially closed?

Or, if it closes, locks and can be fired, then what happens when it tries to extract the case?  Is the case sticking in the chamber, or is it pulled from the chamber but not being ejected and hanging up inside the upper receiver as the bolt moves back?

Detail please.  And, yes, a photo would be helpful.

^ This.  Is that first handloaded round not chambering at all or is it not ejecting after firing?

Begin with the rifle bolt down on an empty chamber and no magazine in place.   Load the full magazine into the magwell and hit it on the bottom to lock it in place.  Then rack the bold back and release.   Does it chamber the round, or is it failing to strip it from the magazine?  If it strips it from the magazine, does it chamber, or is the bolt only partially closed?

Or, if it closes, locks and can be fired, then what happens when it tries to extract the case?  Is the case sticking in the chamber, or is it pulled from the chamber but not being ejected and hanging up inside the upper receiver as the bolt moves back?

Detail please.  And, yes, a photo would be helpful.

The first round strips out of the clip fine but does not chamber completely ? I'm full length sizing the cases with 5.56 dies. The only thing I can see that matbe hitting on the case is the lead tip on the bullet. The bullets are seated to the correct COL, should the bullet be seated deeper because they are lead tipped?

Pictures, man! PICTURES. Is it failing to feed, not going fully into battery, bullet getting caught on the feed ramps? Do you have the same problem if the first round is on the other side of the magazine? Have you tried different magazines?

The bullets are seated to the correct COL, should the bullet be seated deeper because they are lead tipped?

I agree with post above that you should not go deeper than specified COL.  But, this can be confusing because different manuals have different COL listed.  It's just what the manual used for testing pressure. 

What manual are you using and is your load anywhere close to max?  What is the COL you are using?   I think the shortest I've seen in the manuals I use for 55 grain bullets is 2.220" which is what I'm using for Hornady 55 grain FMJ plinking ammo in LC cases over 25.5 grains of H-4895.  This is well short of max magazine length, but does ensure reliable feeding (100%).

Some on-line manuals are showing 55 grain bullets seated as short as 2.200", but I don't know what charge weight of 4064 you are using, so I can't comment on pressures, and every rifle is a world unto itself when it comes to handloading.