The brass is Weatherby brand stamped 338-06 A-SQ. The firing pin protrusion was .062 and the same box of primers had no issues firing in my 338 Fed. or .260. Also I used the same tool and shell holder to prime those 3 different cartridges. I'll list all the measurements I took from gauges and case.

New unsized brass 2.041
GO gauge (30-06) 2.044
fired brass 2.047
NoGo gauge (30-06) 2.049

The fired cases were de-primed before measuring and the bolt was clean, very lightly oiled and had no over spray. I'm still thinking it's a brass length vs head space issue. I had a 338-06 Imp. in an Encore rifle I had to fire form cases for a while back. This time I went with the regular 338-06 so I wouldn't have the hassle of fire forming. Oh well. I think in the next week or two I'll fire form 10 cases and see what they measure afterwards and see if I get any misfires. At least then if I sell it it has brass that won't cause misfires.