The stability calculator
http://www.jbmballistics.com/cgi-bin/jbmstab-5.1.cgi shows the following:
You want a Stability Factor S.F. of 1.5 or greater - higher is better.
39 grain, .733" long, .204 bullet at 3,500 fps in 1:12" twist has a Stability Factor (SF) of 0.858 - unstable.
at 3,400 fps S.F. = 0.850 - unstable. The slower it goes, the worse it is.
This bullet can't be shot fast enough in a 1:12" twist to become stable - it's a waste of time, even at 4,000 fps. Cleaning the barrel is a waste of time.
A 1:11" twist at 3,500 fps the 39 grain bullet is marginally stable with a S.F. of 1.022. Getting there, but no cigar.
A 1:10" twist at 3,500 fps results in a marginally stable 1.236 S.F.
A 1:9" twist at 3,500 fps = a stable 1.526 S.F.. There we are, finally stable.
I use a 1:8.5" twist for anything above 35 grains and the 39 grain bullet would result in a S.F. of 1.711 at 3,500 fps.
My test results show anything less than 1:9" will produce instability with heavier bullets, or longer lead free bullets. The 1:8.5" twist shoots Berger 50 grain HPBT bullets very well. This applies to the .224 and .243 bores as well. The jackets aren't rupturing, the bore isn't rough or fouled, the twist is just too slow. In fact the factory 1:12" twist is a complete disaster for shooting a wide range of bullet weights and lengths.
We can all prattle on about this or that theory but I found that it works to just plug the bullet length, diameter, weight, velocity and twist rate into the JBM calculator and go from there. It has never set me wrong. Even the little 26 grain Varmint Grenade shoots amazingly well in the 1:8.5" twist at 4,110 fps. Quarter inch all day, and only because I can't shoot better than that. Bottom line, the 39 grain BK's aren't for you, try something else, or order a prefit 1:9" or faster Savage prefit barrel and swap it in.
Oh, also don't worry about "dirty powder" Reloader 10x, it shoots superbly in both my .204 Ruger and .223 Remington. Its the closest thing to an ideal powder for these cases. I clean with Bore Tech's Eliminator, then Cu2 Copper Remover, then C4 Carbon Remover. A few patches is all it takes.