One possibility is that if the JTX1 is mixing an earlier release with the R24.1 you are restoring there could be another incompatibility. Can you flash to R24.1 first to verify regular flash works? Then restore (tegraflash.py does not do everything the flash.sh script does, it is a subset…first doing everything and then just the rootfs clone restore guarantees it all matches).
One option is to do a normal R24.1 flash rather than directly using tegraflash.py, but add the “-r” option to reuse system.img (essentially flashing everything but never using the default sample rootfs…this would go directly to your clone rootfs). You’d have to put a copy of your root partition clone in “bootloader/system.img”. Just be careful to not destroy your original image. Note that if you had a specific size used for your root partition when originally flashed it might be useful (I’m not sure) to explicitly use that same size argument during the flash with restore option. E.g., something like this if you used maximum partition size in the past:
sudo ./flash.sh -r -S 14580MiB jetson-tx1 mmcblk0p1