Yep, I had that happen recently. I went with your suggestion no.1, took the crank back out and filed a small chamfer on the ouside edge (no angle grinder reqd, just a good file). The original nuts have a smaller diameter lockingn ring on top, while the SRM (ARP) ones got the hex going over the full width, that's where the problem comes from.
When did you buy the bolts? I have reported the problem to SRM end February, and they promised to add a note to future sales. If they didn't do it, I am gonna have to drop them some bad bad notes....
HTH, Markus