Hey Mike, that is mystifying. If your modified case had some headspace then the bullet should have been further from the lands on your loaded round, but if you are loading new cases and your ejector button pushes the case forward that could have been part of the problem.
Hard to get all those moving parts and moving dimensions sorted out in my head. Perhaps your modified case was not seated fully, case shoulder to chamber shoulder. Tight necked custom chambers can cause that and I have had to outside neck turn a modified case to get it to work.