Yes, this needs to be something that you can turn off separate of the Thread URL Rewrite. However, I figured out a solution that seems to work fine. I now rewrite the Last Post and Newest Post markers to their ORIGINAL URL.
In the custom box for Newest Post and Last Post I put:
showthread.php?goto=newpost&t=[thread_id]
showthread.php?goto=lastpost&t=[thread_id]
This restores the original URLs for these items. After doing this, I reinstated Cookie based forum marking. So far, all is well.
I've asked in the URL Rewrite forum if this is going to cause any future problems but have not received and answer yet.
Obviously, a better solution is to have the option to not rewrite these URLs.



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