Hello,
the ARTIO metabot does not really "rewrite" anything. It just takes the meta information you have defined for your URLs and puts that to the meta tags in your page header. It does not modify the data in any way.
Also, it works only with metas and page title, so it does not interfere with the page contents at all. What you are writing about sounds to me more like a problem with correctly set encoding. This kind of behavior is quite typical e.g. in cases, when you use latin1 in your site administration and then you show the page in UTF-8.
But maybe I am wrong, however I cannot imagine how JoomSEF could cause what you describe. If you could paste link to the problematic pages, it might help.
Best regards,
ARTIO Support Team