I've been using "Not Scripts" v0.9.6 extension in Chromium browswer (currently v30.0.1599.101) from the last one month and found the extension extremely useful. However, after reading some tracking issues related to cookies, I decided to clean off all the cookies since the beginning and switched it to option "Block all cookies including third party as well". With no exception, I found that when this option is selected for cookies, the "Not Script" virtually get bypassed on every website rendering the extension useless for its purpose. I tried to post this question on their mailing list but someone already asked the same and received no answer. May I know why exactly this problem is arising as I don't what cookies in my browser unless for Gmail and Facebook [only for sessions] ? Similar situation in Firefox with "NOSCRIPT" addon doesn't create any mess.
Not technically an answer to your question. But the Not Script extension for Chrome has not seen any development since 2010. I would recommend trying the Script Safe extension as a replacement. It uses a new script blocking API which was released after Not Script ceased development. A quick test on my computer seems to indicate it will work perfectly fine with cookies completely disabled.