Sometimes applications will create windows which are not immediately visible to the user. These windows may serve a variety of reasons (processing Window Messages etc) and may be obscured from the user in various ways, by being hidden, transparent, or zero sized.
Some windows may have a transparent look without having the WS_EX_TRANSPARENT style associated with them. These windows will typically allow whatever is underneath them (for eg. the user desktop) to "come through" in normal operation, and may be used for other features of the application (eg. pop-up messages).When run in a full desktop, these windows do not pose any problem. However, when run in a seamless session, these windows may cause some issues. In seamless, a transparent window can only show the content which is directly behind it, which is likely the user desktop. However, when the window is re-created on the client machine, it will not be transparent, and therefore may appear on the client as a black area (or some other color, depending on the user desktop wallpaper).
It may be possible to hide this window from view (depending on the properties of the window) using some per-application Seamless Flags, such as:
In order to confirm if any of the above flags would be effective, you should run WindowHistory of WinSpyxx to check the Window class and it's associated properties and styles. Additionally, a window that appears transparent may actually be part of a larger window, which is not transparent. In this case, there is no method in seamless to hide part of this window. The current seamless implementation only allows for windows to be either Displayed on the Client, or Not Displayed on the Client - there is no option to only draw part of a window.