Initially I suspected your recoil spring was too stiff for the ammo your were using from the discription of the symptoms. The extra info you wrote about your pistol tends to confirm my suspicions. I suspect that the recoil spring is too strong for the power of ammunition your shooting.
My diagnosis of the problem as you've describe it is lack of sufficient bolt speed is causing the stovepipes. A bolt traveling too slowly will not be able to expel the empty case with sufficient force and speed to clear the ejection port in enough time to avoid the bolt closing on it.
Now the reason those two mags work can be as simple as their feeder springs are weaker than the others and this causes less drag on the underside of the bolt as is cycles rearward during recoil.
I don't suspect that anything your experiencing is related to the aftermarket VQ parts you've installed. There is very little they do that is related to cycling of the bolt. The only thing that could have had an impact would be a higher tension hammer spring because the bolt would have to overcome that tension to push the hammer rearward and recock it. I don't see this from your description.
The reason I asked about your magazines is if the tensioning fingers (tabs) were too tight on the top round in the magazine then this would also slow down the bolt while its traveling forward in the extraction/insertion cycle.
The remedy to the problem more than likely is to remove a few coils from the recoil spring. One or two coils should do it but don't go any higher than three. The down side is you'll only be able to shoot the lower velocity ammo in your gun, not a problem if that's the kind you shoot anyway. You could also purchase another recoil spring assembly and leave it set for the high velocity ammo if you want to shoot that stuff later. Changing out a recoil spring is a very easy task with a Ruger Mark II.