The difference is due to an improvement in the image quality. In ArcIMS 4.0.1 a change was made in the ImageServer that affects image generalization.
In ArcIMS 4.0 the default accuracy for image generalization was 1 pixel. In ArcIMS 4.0.1 it has been changed to 1/64th of a pixel, so the image generated is more accurate now.
If you wish to set your ArcIMS service to have the same generalization as it had in ArcIMS 4.0, you need to add or modify this line:
<IMAGEGENERALIZATION mode="1" />
in your *.axl file in between the <PROPERTIES> and </PROPERTIES> tags and refresh your service.
For more details and an explanation of image generalization, please see information on the IMAGEGENERALIZATION tag in the ArcXML Guide for ArcIMS 4.0.1.