...mmm.. your question is not clear for me.
Can you describe your system? Java, .NET, C++/Qt or what else?
Does your dockable window work in your environment without the ArcGIS Engine?
Cheers (from Italy)
Andrea
Your docking window works in ArcInfo because the framework for it has been built by ESRI. Your ArcEngine application doesn't have a docking framework automatically built in - you have to (and can if you are patient enough) create it yourself.
Here is a free sample to download that can hopefully get you started. There may be others.
Good Luck
Brent