If you use autotoilet at all, you should use the snap functions. But, just because you can preset automatic snap to intersection, endpoint, midpoint, apparent intersection, and so on, having too many of these running is where the problem arises. There are instances where you may be in a hurry, and clicking just so, will confuse the program. It will send a vector off into either Z+ or Z-, but look like it connected with the target, and the problem becomes cumulative.
In the 2007 and up versions there is a properties side window, by which you can modify a lot of values. Doing a box select without an initial command will display the grips. Expanding the properties side window will allow you to step through the entities types to verify their start and end values, their z values and so on. You can overwrite or edit in some of the fields.--Just another method.