Generally, we recommend the following steps when making a scanner profile.
Clean the scanner bed
Make sure the iT8 target is free of dust or scratches
Scan the tiff at 200 ppi at original size
Don't use any sharpening, color management, or color enhancements in your scan
If possible, set the histogram to full range
Open the tiff in Photoshop and remove any dust or scratch spots in the patches (cloning, healing brush, etc.) If the image is a little crooked, try to get it as straight as possible
When you crop the tiff in your profiling software, crop just inside the corner patches so that you don't get any of the border color. Use the zoom tool in the lower left of the screen to be sure that you align the crop properly.