...isn't quite working as it should when done via the link that goes with "2" at the top of the screen.

Here is an example: http://www.skepticalscience.com/thread.php?t=166&r=82

If you try to go to the 2nd page with the link at the top, you end up on an empty page with only the correct information about the entries (eg. "Posts 51 to 83 out of 83") and "post a reply" fields but not the thread-content.

The link shown is
http://www.skepticalscience.com/thread.php?Current_Page=2&Total_Rows=83&&ThreadId=

It works as it should on the corresponding link at the bottom of the page:
http://www.skepticalscience.com/thread.php?Current_Page=2&Total_Rows=83&&t=166

The only difference I see is that the first link doesn't show the thread-ID as "T=166"....

This most likely doesn't have a big impact as there aren't (m)any other threads which have garnered 50+ replies, just thought I'd mention it.

Cheers
Baerbel