Try different skin, possibly there is such which will fit better in to your environment.
Alternatively, you can create a new skin, which will look like a standard OS window. We have brief instructions for that here - http://www.vladonai.com/allmynotes_app_link_skins.php. For the beginning would be enough to create frame only, which is probably not that much work.
We actually count it as a huge advantage that AllMyNotes has skins, yet we don't have enough time to create many new skins, but over time there will be more, hopefully much more. This is the key point of our strategy - to make our software pleas an eye. Very few software titles can do that on their own, it's a big piece of work, it took us 2 years to do it from ground up.