I agree. Avoid automatic modes whenever you can unless you are making a "quick and dirty" scan.
Software that makes adjustments and crops automatically usually makes educated guesses about the material you scan and can often guess wrong. The only way to force the computer to record what you want is to use manual mode.
If you quickly want to scan things to make contact sheets with or to put a low-rez version on your web page, automatic modes are usually okay but they aren't very good for high quality work.
Secondarily, I think you should consider using different software for your scanner. SilverFast and VueScan are two good ones.
At the VERY MINIMUM you should read the websites and do some research for yourself.
http://www.silverfast.com
http://www.hamrick.com
I started using Hamrick's VueScan and I never looked back.
