Can you at least post a screenshot of your home page layout for us? You can blur out the address and text, etc so we don't know the site. Thanks. This thread is pretty useless without something we can chew on!
I do not understand why you are worrying. be happy for the increased clicks, why in the world do you think they are illegal ?
At least you have contacted Adsense. So if they close your account then you can say that you contacted them as you were worried about this and they replied that they can't mention anything about the clicks apart from they will watch the account. Now what you have to think to yourself, does your CTR look reasonable or rather high. You can't discuss CTR here unfortunately as it's against Adsense TOS. Another thing is if your homepage is getting alot of traffic, which is normally the most visited page on alot of sites mainly because this is the main page that people advertise and also that your visitors will always look at, then don't forget you have put a new ad at the top of the homepage. That will result in an increase of CTR compared to an Ad that is situated near the bottom or right-hand side of the homepage. This is because the top ad is likely what your visitors will see first before they see anything else if it is right up the top. Although I have not seen your site, I just have a feeling that this is what it could be. Although your CTR is very low, it could also be the topic of your site, is it an entertainment related site or something?