This is the weirdest thing.

I am using links2 as a download centre.

During one of my updates, all was going well, I had built the database twice. Then when I went to build for the third time I got a bloody 500.

I went back and tryed again, the whole admin.cgi was a 500 same with the search.

Any ideas,

Difficult to say without further info. Have you checked your error logs? Or your permissions? Have you added any additional modifications before the error occured?