Nope, thats just the problem running the ARP's. Almost every company ive talked to say that when using them the block main bores must be line honed as the studs take a different affect on the block compared to bolts.
I doubt he has the caps on backwards as the last person to do that cracked his block trying. The caps will only properly go on one direction. You should have them in numerical order. 1 being at the front of the motor, top of the numbers point to the front of the block.
They were designed to be in their original place. So ensure thats the case with yours but i would strongly recommend just using some new GTIR main bolts (stronger than the stock main bolts) as they are cheap and just as strong as the ARP's. Im using them and have had zero problems.
Again its basicly impossible to put the cap upside down as the grooves that were cut wer cut to length on the caps. They will not want to seat down right.
But like i said your problem is plain and simple as your using the ARP main studs. Again, not necessary and only causes hastle. It would be cheaper for you to get the GTIR mains than to line hone the block. Less time im sure as well. GregV has them. Talk to him.