@mikey : I've had A TON of grief caused by free templates that had my links in them ( [webmasterworld.com...] ) and my tussle with Google over that was successful in only 1 case out of approx. a dozen sites similarly affected.
So, netmeg is asking a very valid question: if your links are embedded in the templates that you let people download, then Google may see this as unnatural links. You may be able to convince them otherwise by insisting that you are the actual designer and even then, I think you will do much better if you create new versions of your templates with your link no-follow'ed and tell Google about these new ones, maybe you have a chance then.
But as far as grossly unmatched AdSense ads - this in itself is a huge red flag. I mean, first of all for you as a webmaster, I'm not sure if Google cares much about those ads in terms of the penalties. It can mean that your site has been hacked and the hacker is now sending tons of keyworded links to the hacked pages. Probably from hundreds of forum profile pages and the like. That, by the way, could also easily trip the inorganic links filter for Google. This happened to me before: a site that had nothing to do with pharma, started to show ads for various [dubious] drugs. I chucked it up to bad AdSense matching algo but I should not have been so quick to dismiss it. It turned out that AdSense's relevance is so much better than Google's own SERPs, ironically.
My site had one page (just one out of hundreds!) hacked into via comments and links to places that sell drugs seeded. Then they threw hundreds of forum profile, blog comments and other low quality keyworded-anchor links to that page. This one hacked page and the massive amount of links with drug-related anchors was enough to skew relevance of AdSense ads on the entire site!
So, if you are seeing grossly mismatched ads, don't just ignore it, it may be an indication of a bigger issue - your site may, in fact, acquire massive amounts of bad links, even if unbeknown to you. Google may be reacting to links that you don't even know about yet. Go through your site's code (as rendered to visitors) with a fine comb, see if you can spot any foreign insertions there and fix that ASAP, then file the RR again.