This is an issue that many people may never run into, but if you do you'll realize it's not fun! The problem comes about when you are using dependant views and you have reference sections pointing to another view and you modify the section mark in it's length and/or head/tail location. If you place a reference section and say stretch it out, or need to change the head to the other side, the section will revert back to it's original placement location (before you made any changes to it) as soon as you adjust the crop region in the dependant view. Please take a look at the attached video for a visual of the issue. This is from an actual project where the person had a lot of referenced sections. The video zooms into the dependant view so you can see the sections changing as the crop region was adjusted.
I've forwarded this issue to Autodesk and at this point "The underlying issue for this case is being addressed by our development team". So if we all keep our fingers crossed, they will be able to fix this issue in a new build or in the next release (2009).
At this point, the only thing I can think of as a work around is to adjust your crop regions first, then adjust your reference sections to be the way you want them. But even then, if you have to make an adjustment to the crop region, all bets are off.