Scanning still fails with the newest version but the messages now accuses
gpilotd clearly:

dmesg relevant part (from connection to deconnection through scanning):

usb 5-1: new full speed USB device using uhci_hcd and address 9
usb 5-1: gpilotd timed out on ep0in
usb 5-1: usbfs: USBDEVFS_BULK failed ep 0x81 len 4096 ret -84
usb 5-1: usbfs: USBDEVFS_BULK failed ep 0x2 len 2 ret -71
usb 5-1: usbfs: USBDEVFS_BULK failed ep 0x2 len 2 ret -71
usb 5-1: USB disconnect, address 9

gpilotd seems to grab the input of the scanner preventing Xsane from receiving
the data.
Suspending gpilotd still solves the issue as a workaround.

gnome-pilot version : 2.0.12-1.1

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