If Nikon's software was a much better option for most people then it would not be the case that nearly every professional digital tech, full service rental studios, and production companies uses Capture One or Lightroom.
Simon, I'd Contact Phase One
to start a support case with Phase One, or, ideally work with a good dealer. They can give you the ins and outs of diagnosing why you're having issues so that you're rock solid from now on. Typical issues include corrupt library files, bad or cheap cables, using too long of cables, bad/low batteries in the body, use of an OS in which all the obscure bugs haven't been worked out of the tethering SDK that Nikon/Canon provides (e.g. I assume you're not using the brand new Mountain Lion for a professional shoot yet).Any
software can crash (trust me - I'm the one that gets the call when it does) but a properly maintained Capture One instance on a solid OS with proper cabling is rock solid. I know this from consulting with studios that work with several cameras, all day, 5 days a week, all year.