I'm seeing the two problems with version 4.1.3...
With "Count All Posts Marked as Unread" set links to search results are broken such as:
search.php?do=getnew[ARG:2%20UNDEFINED]
The above works with "Use last visit date".
I'm also seeing what appears to be the message being repeated:
"You Have 5 Unread
You have %1$s unread %2$s"
And the second link doesn't work such as:
%3$ssearch.php?do=getnew%4$s
/%3$ssearch.php?do=getnew%4$s
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