Can you provide more information about which iMac you have, the version of Mac OS X, and the model of the Brother printer you are using? Have you installed all of the available software updates including those provided by Brother?
I use a Brother laser printer to scan documents without any issues, although instead of using the Brother software I have begun to use the scan features accessible from the Print & Scan System Preferences (I'm assuming you are running Lion since your profile doesn't say). After opening the Print & Scan System Preferences click on your printer in the Printers column, then click on the Scan button on the right side of the window. Specify whether you are scanning from the document feeder or the flatbed, then click on the Overview button to do a pre-scan. I have been quite satisfied scanning this way.