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Problem when processing a pre-defined area. HELP.

I have a problem when trying to work with a pre-defined processing area (KML):
I noticed that when the project is NOT translated to a Calibrated Arbitrary Coordinate System (i.e. is an Auto Detected WGS 84), I can draw and import a polygon to define a processing area without any problem and the processing works great.
But, when try importing the polygon on a project that is translated from its creation, the import (under Map View > Processing Area) is greyed-out so I can’t click on it (It doesn’t allow me to pick an option). Is this normal or is something wrong with this?
I also tried creating a project without translation then import the polygon (so far so good) and then translate the coordinate definition. The result was half of the project was outside the polygon, so it is not useful.
Is there any way I can sort this out?