Re: Strange issue
46 grains of Varget is a mild load- have had a run of .308's through the workshop of late and all reach absolute max (but still OK) at 50 grains compressed with mild pressures at around 48 grains. That said, All were Remingtons which have a freebore of 100 thou. On the other hand, Varget is very consistent, extremely temperature stable and not prone to sudden spiking when used in low capacity cartridges.
Sometimes, a rifle will have a minimum throat- saw that on an A-Bolt a while back. The throat was too short- even by SAAMI standards. With factory .270 Win ammo, the bolt locked up every now and then.
Regardless, I am constantly being proven wrong by other factors. One of these factors would be seating depth. If you have micalculated the COAL and the bullet is jammed hard in the lands, it will casue pressure spikes and stiff extraction with near max listed loads- every couple of shots. I just had a hunting client arrive with such a load- had his seating die set up for Nosler BT's but loaded a batch of Partitions for the hunt.
Something is definitely wroong and as esshup said, you need a chrony as an aid to pressure/ velocity. It may sound silly but you would be surprised how many times people get caught out by decanting powder into a more user friendly container but then get the labelling mixed up- especially if the label is on the lid. Might pay to double check that.
Someone else mentioned your brass- if it is too long, it will pinch the bullet and trap it in the chamber.
Good luck, if it is human error- you will probably kick yourself, its always the simplest things we overlook. I just had a client wanting to show off his new Sendero to me. He wanted me to look at the bedding block and give it the once over which I did, shaped it here and there, after which I re-assembled the rifle, gave it back to him and continued my tasks for the day. I always make a point of checking that the mag box is not pinching when I re-assemble a Rem but in this case, not only did I fail to check it, I mis-aligned it- idiot. Luckily the client noticed it when he got home. He visited me today and gave me heaps of s---t.