I am trying to register a domain for a customer. When I did so it said it was taken but if I search the Whois database it says it is available. If I search at GoDaddy or Dotster it says it is unavailable.
This has nothing to do with the registrars whois. Some registrars query the registry for availabilty and others query the internic. The internics whois is generally 24-72 hours behind the registry. Registry look ups are real-time, no delays.