It's not so much your scanner that is the problem. You need different scanning software. If you are not opposed to spending a little, RansenScan does a decent job of "batch scanning" multiple objects on the scanner bed. It's $29.99. I own a copy, and the creator is still actively updating it and is responsive to suggestions for future updates. Basically it lets the scanner make a single pass, and then the software either automatically picks out the different objects, or you can do it manually.
http://www.ransen.com/RansenScan/Default.htm