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.
In order to submit a ticket, please shoot an e-mail to (firstname.lastname@example.org) being sure to include your username, and the original cPanel password of your account or the last 4 digits of the credit card on file for verification. Or you can submit a ticket directly through our support interface here:
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Please let us know if you have any further questions we can publicly address here for you as well.
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