Both workflow should give the same results. So this could be bug or file related. Can you post a dummy file created using your workflow to check/test.
Ok, I solved my problem, here it is....
For some reason my parts were being highlighted grey instead of the green when their step is clicked in the config manager.
I did not notice this before though because most of my assemblies and parts are shades of grey.
Back at the Feature Manager Design tree when a part is clicked it does indeed turn green though.
This made it seem like more of a setting issue, so lo and behold under options - system option - color - color scheme settings - highlight
This was set to grey. I changed to green and now all is well.
Thank-you for your willingness to help Deepak.