The problem is that UserControls loaded inside a web  part don't actually know
what type they are because the ascx  is in one place and the dll in another. So
doesn't know its type and can't access  properties directly. But you can access
them using Reflection. Instead of your code  try the following code snip.

protected override  void CreateChildControls()
{
UserControl x =
Page.LoadControl("~/_controltemplates/Custom/MyCustomControl.ascx")
as UserControl;
Type myControlType = x.GetType();
PropertyInfo MyControlProperty =
_myControlType.GetProperty("MyControlProperty");
MyControlProperty.SetValue(x, "some value", null);
this.Controls.Add(x);
}

I'm assuming that MyControlProperty is a Public string property  in the
codebehind file for your user  control.