I have been using a noscript tag to show a warning when users have JavaScript disabled or are using script blocking plugins like Noscript. The website will not function properly if JavaScript is disabled and users may not figure out why it is not working without the warning.
After the latest Google algorithm shuffle, I have seen the daily traffic drop to about 1/3 of what it was in the previous months. I have also seen pages that were ranking #1 or #2 in the SERPS drop out of the results. After doing some investigating in webmaster tools, I noticed that "JavaScript" is listed as #16 in the keywords section. This makes no sense because the site has nothing to do with JavaScript and the only place that word appears is in the text between the noscript tags.
It seems that Google is now including and indexing the content between the noscript tags. I don't believe that this was happening before. The warning is three sentences. I'd imagine that having the same three sentences appearing at the top of every single page on the site could have a damaging effect on the SEO.
Do you think this could be causing a problem with SEO? And, is there any other method to provide a warning to users who have JavaScript disabled in a way that won't be indexed or read by search engines?