Here is a strange one for you – I was setting up a new virtual machine today. I went with 64-bit Windows 2008 R2, SQL 2008 and MOSS 2007 patched up to the April 2009 cumulative updates (18.104.22.16818)
Everything had gone pretty smooth until I went in to create a new Web Application in Central Admin. Lo-and-behold, the link was missing. Hmm, seen this one before, so I got out my favourite search engine and found a recommendation to run Internet Explorer with admin permissions. This seems to have fixed most peoples problems, but not mine.
After a number of futile attempts I noticed that the computer date format was mm-dd-yy. I’m in Australia, so I prefer dd-mm-yy. I updated the Format and Current Location regional settings via the control panel and I kid you not, this fixed it!
Trust me, I understand if you are sceptical, I still don’t understand how this would affect the visibility of certain links in Central Admin. I would be curious to hear if anyone else experiences the same problem and resolution.