When some people register and login it tells them they are offline and will not let them connect. Any ideas? Also on the downloads when they download it just opens the file. What is going on? Do I need to set something?

I had the same problem, a user registered, the activation e-mail was sent out but it was a bad link. I changed my site addy in the preferences section of the control panel to my IP addy. This fixed the activation but when registered users accessed the site using the URL they could not login, same problem as you.
Now then, are you hosting the site on your own server or are you paying a host. I host my own site and the problem was that my URL didn't point to my IP address because I was using webdiversion (UK2).
A change to the DNS 'A' record (the IP that the URL refers to) to my IP address fixed the problem, yours could be the same.

But it isn't every one just some people. Thats what is weird.