I was pounding on it today but couldn't get it to fail with a new model. The error log didn't have anything that coincided with the time when I clicked the ">>" button, which shows in the tree that it's going to create a new column, or when I "Engineer".
Two data points, for what they're worth. One, the engineer comparison tree doesn't show, for the relational model, that the once-new column exists at all. That is, it's not showing the column and showing that it's going to create one. It just looks as if the column doesn't exist so that it's going to create it. Two, when it does create the column with the numerical suffix, it puts it at the end of the column list, not in the middle or wherever the once-new column appears in the logical's column list.
Wish I had more clues.
I figured it out so I thought I'd put this here in case others bump into it.
What's going on is that the logical-to-relational engineering comparison tool doesn't recognize relational columns that the engineering tool didn't create. Sometimes I would add columns to both the logical and relational models manually rather than engineering. Say all I wanted to do was to add an active_flag to a table. I'd add it to the relational model and then add it to the logical model's corresponding entity with exactly the same values. Later, when I had a bunch of logical model changes to engineer, it wouldn't recognize the active_flag ("preferred abbreviation") in the entity as being the same thing as the active_flag in the relational table, and it'd create an active_flag2 column.
Lesson: only create new relational table columns by engineering them from the logical model.