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update what? you might have missed my last couple posts...
Visit Cruise Talk Central and Mr Papa's World
Yes, I did miss them.
I still haven't solved it, but I did these things...
1. Updated my SVN and loaded it to my server, so I am working with essentially the same code you tested.
2. Created a new site on the problem network with the same theme and same set of plugins. SPF worked fine. That rules out theme or plugin conflicts.
3. Took another network on another server and activated SPF on the main site. SPF worked fine. That rules out problems with it being the main site. This site was also running Genesis, so it's another confirmation that it is not theme related.
4. Checked the .htaccess on the problem site, and it seems fine.
5. Navigated to a few of the image URL's in the blogs.dir folder for the main site to confirm I could read them, and all was fine.
All of that suggests it is something particular to the main site on that 1 network. Hopefully, I find a way to make it work.
yeah, like I said, we have lots of folks running genesis...
are these all on the same server? ie all running same server os? and all running same multisite plugins and all using same domain method? ie subdomain or subdirectories?
Visit Cruise Talk Central and Mr Papa's World
The main site test I did was on a different server, but it is virtually identical (Hostgator VPS, both of which I setup by the same playbook). Both were running the same set of plugins (same versions, same Genesis version) and using the same domain method (subdomains). I made a post on the WP forums. Hopefully, I'll get more feedback.
At last! Persistence paid off.
The culprit was this line in my wp-config.php:
define( 'NOBLOGREDIRECT', 'http://www.qbgarage.com' );
Basically, that performs a redirect when someone attempts to visit a URL that doesn't exist. Perhaps SPF is doing something to generate the URL's for the forum? That's why the main forum page loads, but access to the forums triggers the redirect.
The problem is that this is very useful to direct users to the home page of the main site when they try to access a SITE that does not exist, but it creates a problem because of the impact it has on the main site. Therefore, the workaround is to create a script (something like myscript.php) and put it in the wp-content/mu-plugins folder. That way it gets executed like a network activated plugin. The script should contain:
<?php
remove_action( 'template_redirect', 'maybe_redirect_404' );
?>
Hopefully, that will help the next person that wrestles with multisite.
good hard work. Yes, we add url rewrite rules to the wp list... remember all forum content appears on a single wp page... so the appearance of many forum pages is just url rewrite magic...
but it does not generally do redirects (there are some instances where a redirect exists, but not via 404 status)... I wonder... is your permalink for you wp consistent with the forum as far as trailing slash? if not could cause 302 redirect but that should be harmless, just a waste...
Visit Cruise Talk Central and Mr Papa's World
Yes, both show a trailing slash. I am sure it is your URL rewrite magic that caused multisite to get confused. I should have thought of that earlier when it was only happening on the main site. It just took so long to wade through all of the other differences, like plugins, that are the usual culprits. I'm glad it is working now and can get on to more testing.
Thanks for your steady help.
no worries. glad to have someone putting it through the wringers. Not sure why multisite would be confused, though must admit never used or heard of that define you used... 
Visit Cruise Talk Central and Mr Papa's World
Confused might not have been the best choice of words.
This is from the settings page of the network admin:
If registration is disabled, please set NOBLOGREDIRECT inwp-config.php to a URL you will redirect visitors to if they visit a non-existent site.
Without that setting, a visitor to a non-existent site either sees a strange message of:
Greetings Site Administrator! You are currently allowing “none” registrations. To change or disable registration go to your Options page.
Registration has been disabled.
if you disabled registration or they are taken to a sign-up page based on your registration settings. Many network admins consider that less than ideal behavior, which is why there is the NOBLOGREDIRECT directive. How that directive gets implemented is where the confusion comes from. Even ignoring SPF, adding that directive alone without the small script in mu-plugins wipes out 404 errors on the main site, because they get directed to the home page.
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