Ubuntu

I have a laptop running Ubuntu Gusty. I have recently used applications such as AWN, Emerald, etc... to create a Mac OS X Leopard like environment. It works almost perfectly except for one little glitch. When I open most of my apps/windows, they all open with the top bar(with includes close, maximize, and minimize), sorry I just don't know the real name for it, under the top panel. I don't mind using alt+mouse to move the windows when this happens. I just wanted to know if it is possible to fix this because this is starting to get annoying .
Any help would be appreciated. And can someone tell me the name of the bar.

It sounds like the title bar.

Can you post a screenshot for confirmation?

I don't have a screen shot on my comp, but I do have one on Deviant Art. Here's the link. sorry bout the black lines. confidential info.

Now it's being really annoying. The title bar is now disappearing. I can fix this by using Alt+Ctrl+Backspace and sign in, but this gets annoying when it goes down when I'm using VirtualBox OSE and I dont want to have to end it and have to restart it.
please help

You mean they start with just the title bar visible, and the actual window hidden? Just a clarifying question; I have never seen anything like this (and would tend to blame the OSX "costumizations" probably).

It doesn't do it anymore really. But what it was was that the title bar(the one with min, mac, and close) would be covered up as if the space that it could open up in was enlarged but it doesn't anymore. Once I changed the pointer settings, it got fixed. I'm not sure why, I think it was just some configuration settings that need clearing up that I did.