In the 64 bit IDE, the micronucleus executable in hardware/digistump/avr/tools appears to be 32 bit not 64 bit. This causes it to look for a 32 bit version of libusb. I do not have the 32 bit version installed, so it failed to run. The copy in linux64binaries.tar is also incorrect. It matches the version in linux32binaries.tar. The workaround is to install a 32 bit copy of libusb somewhere in the IDE's path.