Did you create 'Distribution' or similar configuration to make Ad-Hoc and App Store archives?
Like many others I followed Apple's recommendations and dubbed 'Release' configuration, called it 'Distribution' and set different signing rules to it. Well, maybe that was a recommendation before they introduced schemes and "Distribute" option in Organizer, anyway, I just had it from before.
Then I had same problem with Pods. It all worked well when debugging, but archiving failed with link error. After trying this and that I changed Archive configuration of my original project from 'Distribution' to 'Release' and the link error was gone.
Yet the archive did not show up in Organizer, though I could locate it in file system, but it had 0 size.
Final step to fix all this was to change "Skip Install" setting for 'Release' configuration to "NO". Note, that you have to do this only for your main project, but not for Pods project. Better leave Pods project as is, since it's generated every time you run 'pod install'.
Update
Just got an answer from CocoaPods devs
It doesn't seem to work for me, since I had Pods configuration properly set.
But it could help someone else.