I am scanning with iscan as a Gimp plugin. When I put the negative on the edge of the scanner glass the scan comes out with about an inch of the image not there. The scanner is apparently ignoring an inch on the edges of the scanner glass. I had previously used Image Scan under Windows and I did not have this problem. I am using an Epson 4990 scanner.
Any idea what my problem is?

I'm not familiar with Iscan...whoops, Google is my friend after all!

I took a look at the list of supported scanners for SANE, the scanning API used by iscan and xsane. Which particular Epson 4900 are you using? The listing shows 3 versions of the scanner and two driver backends with various levels of compatibility.

Being a Linux user myself, an issue I had to deal with in xsane is that it uses the top-left corner as the selection origin for the image (top-right on the glass), rather than top-left as the way HP designed the scanner and how it operates under Windows with the HP software. If you are just performing page-size scans it's not a problem, but if you use selections in the preview it's odd.

Of course, this is probably no help to you at all.

No, but it was nice of you to reply and make an attempt. I hope other do also. I bet if enough people say things, someone will have the answer.