When I digitize in the stereo window, the result match with the stereo model, but in the ArcMap window it doesn't. In the Stereo Window the features are right on spot, but I see a shift in the ArcMap Window. Is this normal?
This is normal. Because the images on the ArcMap Window are not orthographically correct and they cause confusion when features don’t match in the ArcMap Window. What you can do is to enter an elevation source when importing the project (if you have a DEM). On Import Photogrammetry Project Wizard click on any "Elevation Source" cell array and enter a raster or TIN surface (please refer to the screencapture below). So, when images are rendered the elevation source will be taken into account. But you may still see some mismatch depending on the DEM accuracy.
Or, you may choose not to import images to ArcMap Window at all. Then you may prefer to import your photogrammetric project (.blk file) using Block File Image Pair Manager because it specifically does not load Images into the Map Doc.