2012-10-12 3:52 pm EST
The permissions should be set properly to allow WordPress to manage these files for you with  as is currently set. I also can see on one of your testing add-on domains that you've installed W3 Total Cache, and it seems that WordPress placed the Rewrite rules for that plugin in the (.htaccess) file, so it seems like it was able to modify that file which had the same permissions.
In this case this issue might be best handled directly over a support ticket so that you can disclose your WordPress administrator credentials to us so we can try to replicate these issues for you and see what might be causing the problem.
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