I recently updated to gscan2pdf v2.6.5 on Linux Mint 18.2 (downstream of Ubuntu 16.04).
After updating to this version, changing the paper size value in the scan dialog (https://i.imgur.com/hqGQvmm.png) has no effect. By default, this value is set to US Letter and pages are scanned with that size (which is the geometry I need most of the time). However, when I change the paper size value to US Legal and scan a legal size document, gscan2pdf still uses the US Letter geometry (which cuts off the bottom of the scanned legal-size pages).
On further investigation, I can select Manual for paper size and enter alternate dimensions (such as the paper size for US Legal), which then works when I scan a document. However, to return to US Letter or any other geometry, I then need to edit the paper size in the Manual paper size editor again. Therefore it seems the US Letter / US Legal paper size option values simply have no effect when selected in this version of gscan2pdf.
Please start gscan2pdf from the command line with the --log=log option, scan a page in US Letter, switch to US Legal, scan another page, quit, and attach the log.xz file so that I can take a look.
Here's the log from my test run.
This sounds very similar to my issues reported in Bug 346.
Thanks for the log file. After a great deal of head scratching, I've fixed the problem for the next release, which I expect to cut in a couple of days.
Awesome, thank you!