Here is a scenario to consider. If you took your fork in to get the steerer tube cut and you said, "Leave this 1cm spacer on top," you might have a steerer tube cut with a 4mm gap between the top of the steerer tube and the top of the 1cm spacer. As long as you used that big spacer, you'd be fine. Now suppose that you wanted to move a 5mm spacer from below the stem to above. If you put the 1cm spacer on top first, then you'd only see 1mm of steerer tube peeking out over the top of it. It would be tough to get the 5mm spacer to work above the 1cm one. The solution would be to put the 5mm spacer on first, but you might first run into the problem that I think the OP was having. A lot depends on the spacers and the nature of the steerer tube cut.