It expects RewriteEngine on to be first, followed by RewriteBase, followed by RewriteRule. Whereas you for some reason have RewriteRule somewhere in the middle of your file before RewriteEngine/RewriteBase.
I'm sorry this isn't reflected better in the warning message. I'll try to improve the message for the next version of Google SEO.
Ok. I see... So what should I do now to fix the problem?
As I said, put the entries in the right order
RewriteEngine
RewriteBase
RewriteRule
RewriteRule
...
Or you can just ignore it as long as everything works.
Well I already did that. I will just assume the plugin is working correctly now... Don't know where I should see that it doesn't.