I must admit I have had a similar difficulty. It's always on a large and complex file and it causes no end of frustration, usually resulting in misaligned edges or verticies early in the project that aren't found until later in the project. By then the damage is done and the work takes forever to repair or redo. I wish I could blame some SU glitch, but I'm afraid it's likely my fault for the reasons Jean says.
I get around it by making the base geometry I'm working with a component. That way I can use it as a "work surface", and there is almost no risk that I will accidentally change the geometry while working on the rest of the project.
Don't know if this helps, but I feel your frustration!