Wow, this is a really long thread. I tried to read everything but I kind of got lost around page 30, so forgive me if this has been asked and answered.
We just installed 5.3 with Threads 6.2.3, and we love it, and you've done a great job. But we can't get the "profile spotlight" to display consistently. We've set all the directory and file permissions as you specified earlier in this thread. The change happens but then on reload the profile spotlight is gone.
We've tried changing cache times, removing some or all of the checked profile fields, and nothing. Last night we did isolate this, however: if you use the "index.php?Cat=&RefCache=1" extension, the profile loads just fine, and in fact it will refresh if you refresh that page. Any other URL ("index.php" or whatever) displays the page without the profile spotlight.
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