The Core Tweaks plugin is primarily used setting up new sites in what we believe is the "right way", and that includes error reporting. That's also why we recommend you have no other plugins active, because then you'll see no errors.  

Since, however, the plugin does turn on your general WP error reporting, if there are plugins giving errors that they've "hidden" from you, then you'll see those errors.

So, given that its WP-ecommerce that's throwing your error, and disabling our plugin will "re-hide" that fact, because we have no option for turnong off error reporting… YET. We will for the next release… Sorry for the scare…. 

Warning: Call-time pass-by-reference has been deprecated; If you would like to pass it by reference, modify the declaration of do_action(). If you would like to enable call-time pass-by-reference, you can set allow_call_time_pass_reference to true in your INI file in /home/content/01/6099701/html/wp-content/plugins/wp-e-commerce/wpsc-includes/cart.class.php on line 881

Warning: Call-time pass-by-reference has been deprecated; If you would like to pass it by reference, modify the declaration of do_action(). If you would like to enable call-time pass-by-reference, you can set allow_call_time_pass_reference to true in your INI file in /home/content/01/6099701/html/wp-content/plugins/wp-e-commerce/wpsc-includes/cart.class.php on line 1052

I'm sorry for the confusion, Freedom...

If you want to try an edit yourself on the core tweaks, I can pin point where the issue is coming from by the code you showed above.

Open settings.php from the seo-automatic-wp-core-tweaks directory.

Scroll through the code till you see include('permalinks.php');

and comment that line out using // before the word include.

This should stop your error. That particular file only runs when you use the setting to change your permalink structure using the core tweaks settings page. It attempts to edit your htaccess automatically.

Fatal error: Cannot redeclare got_mod_rewrite() (previously declared in D:inetpubvhostshidden.comhttpdocswp-adminincludesmisc.php:17) in D:inetpubvhostshidden.comhttpdocswp-adminincludesmisc.php on line 19

Contents of the file affacted are :

I don't get any errors when this plugin is not installed/activated and this error only shows up when I try and go to the Core Tweks Plugin section and not the Admin section.

Since the DDSitemap Generator is part of Core Tweaks, it will not allow you to activate both at the same time. Which is the way it's suppose to work. When using Core Tweaks, DDSitemap Generator should be turned off. Core Tweaks already has it turned on and it is the latest version.

I was unable to find a plugin with the name Site Navigation. We need the actual name and link of that plugin to see where it conflicts. Other people reported that using additional sitemap plugins such as NAVT were not a problem. But the DDSitemap Generator is already included and active when Core Tweaks is active.

If core tweaks works on it's own just fine, and if the functionality of site navigator is built in, then why do you need both? 

Also, deactivating Core Tweaks doesnt UNdo anything that running it the first time in the first place did, s oyou could just leave it inactive.

I'll leave the error decoding to Heather, but you should know that she's on vacation this upcoming week, and she may not see it for a while...

I am getting these errors coming up when I activate core tweeks.  The first time I activated it everything was fine, I then added anther plug in - site navigator and uninstalled core tweeks as site navigator didnt work properly and I also realized you had this included.  When I reinstalled it comes up with this and it has it above my website online also.  Can anyone shed any light on this for me??  Cheers

Warning: include(/home/trotti1/public_html/wp-content/plugins/seo-automatic-wp-core-tweaks/lang/english.php) []: failed to open stream: No such file or directory in /home/trotti1/public_html/wp-content/plugins/seo-automatic-wp-core-tweaks/sitemap-generator.php on line 50

Warning: include() []: Failed opening '/home/trotti1/public_html/wp-content/plugins/seo-automatic-wp-core-tweaks/lang/english.php' for inclusion (include_path='.:/usr/lib/php:/usr/local/lib/php') in /home/trotti1/public_html/wp-content/plugins/seo-automatic-wp-core-tweaks/sitemap-generator.php on line 50

Warning: Cannot modify header information - headers already sent by (output started at /home/trotti1/public_html/wp-content/plugins/seo-automatic-wp-core-tweaks/sitemap-generator.php:50) in /home/trotti1/public_html/wp-includes/pluggable.php on line 865

I ran the validator on your site and the main doctype declaration is missing from the first line of your header. There are also some javascripts added to the source code at the very beginning before the <html>. That needs to move after the body tag to validate properly.

You can see the validator results here:

I use Core Tweeks on my site with veryplaintext and Core Tweeks causes my site to display in IE incorrectly.

Thanks

Lance