I have an issue somewhat like that, except it doesn't happen when I shut down or restart my computer. Mine resets each time I click the green resize button (using an iMac) to minimize iTunes to the mini player. Oddly enough, if I resize the cover flow, switch to a different view (ie. library without cover flow) and then hit the resize button to switch to mini player, upon maximizing iTunes again, I can switch back to the cover flow and it will have stayed the same size. Obviously I'm not going to go through that process each time I want to minimize iTunes to mini player, but when I simply minimize it when in cover flow view, as you mentioned in your post, it resets the aspect ratio each time. Clearly this isn't a massive issue as I'm still able to use all the other functions of iTunes perfectly fine, but I have to admit it is very annoying and has been persistent for the last few hours. Please if you've found a fix let me know, however I noticed you are using Windows 7 so we likely have two completely different issues.