Hi,

>> > Argh, my 2480 is changing to 5.5cm by 7.5cm (judging from the
>> > preview window). Debug log attached.

Your boundaries are fine. From the output of your scanimage command:

> ? Geometry:
> ? ? -l auto|0..55mm [0]
> ? ? ? ? Top-left x position of scan area.
> ? ? -t auto|0..125mm [0]
> ? ? ? ? Top-left y position of scan area.
> ? ? -x auto|0..55mm [55]
> ? ? ? ? Width of scan-area.
> ? ? -y auto|0..125mm [125]
> ? ? ? ? Height of scan-area.

> I posted a screenshot:
> http://thewizardstower.org/sshot.jpg

It's just the xsane logo that doesn't fill the complete scan area. 
There should be no problems with scanning in transparency mode.

/Oliver

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