I'm really confused

This looks good to me except that you have two else statements right next to eachother.

I'd try this:

when HTTP_REQUEST {
  if { [HTTP::uri] equals "/" } {
    if { [HTTP::cookie exists LtpaToken] } {
      HTTP::redirect "http://[HTTP::host]/wps/myportal"
    } else {
      HTTP::redirect "http://[HTTP::host]/wps/portal"
    }
  }
}

Have you determined what exactly your problem is? I'd try throwing in some log statements to find out what's going on.

when HTTP_REQUEST {
  log local0. "URI is [HTTP::uri]"
  if { [HTTP::uri] equals "/" } {
    if { [HTTP::cookie exists LtpaToken] } {
      log local0. "Cookie LtpaToken exists, redirecting to http://[HTTP::host]/wps/myportal"
      HTTP::redirect "http://[HTTP::host]/wps/myportal"
    } else {
      log local0. "Cookie LtpaToken does not exist, redirecting to http://[HTTP::host]/wps/portal"
      HTTP::redirect "http://[HTTP::host]/wps/portal"
    }
  }
}

Then take a look at the /var/log/ltm file on the BIG-IP to find out what's going on.

-Joe