Hey, I've recently had this problem. Seems that you need to replace the 1.0.0 Pcap (the file that works with the firmware version) with a 1.0.1 Pcap. I've found a 1.0.1 Pcap for the EU/JP here:
https://mega.nz/#!LhwhSYRa!FeLXrnvBXgDw6BR7MBNytQ_DN3H-gbMmkYDxQo1d5Fw
You're gunna need to go into the resources folder in the Smashbrohax-helper and then the ones with the Pcap's. Replace the 1.0.0 Other file with the 1.0.1 Other file, and then rename it to 1.0.0 Other. That's so the file can be read by the program, so it thinks it's the 1.0.0 file.
Then go on as normal, just using the 1.0.0 Other version when you need to select the firmware on the Linux program. It should work as normal after that