Ben,
Most likely they set the blank page skipping in the Twain driver originally and it somehow got unchecked.
The following shows the procedure for skipping blank pages using the FUJITSU TWAIN 32 scanner driver:
1. In the [TWAIN Driver] dialog box, click the [Option] button.
The [Option] dialog box app
2. Select the [Job/Cache] tab.
3. Mark the [Blank Page Skip] checkbox. If this checkbox is marked, cache mode is automatically changed to [Ram cache].
4.With the slider control under [Blank Page Skip], specify the Blank Page Skip degree.
<In Binary/Halftone mode>
For white pages, use the [Black Dots Ratio] slider bar to specify a degree of accuracy needed to skip blank pages. For
black pages, use the [White Dots Ratio] scroll bar to specify a degree of accuracy needed to skip blank pages. The
value displayed to the right of the slider bar shows a noise (dots) ratio(*1). If a scanned page includes dots less than
this value, the page is recognized as blank. You can select OFF(- -) or a value from 0.2% to 3.0% (in increments of
0.2%).
*1: Ratio of black dots included in a scanned area. (for white pages)
<In Color/Grayscale mode>
Use the slider bar to specify a level in five levels from 1 to 5. The larger the number, the higher the accuracy.
5. Click the [OK] button. You are returned to the [TWAIN Driver] dialog box.
6. In the [TWAIN Driver] dialog box, click the [OK] button. Changes made are saved and the [TWAIN Driver] dialog box closes.
7. From Laserfiche, perform a scan and see if the blank pages are removed.
It should be noted that if they set this wrong they run the chance of getting rid of good pages with text on them.