I think you need to start pd with the leap library preloaded:
LD_PRELOAD=~/path/to/LeapDeveloperKit/LeapSDK/lib/x64/libLeap.so ~/path/to/pd/bin/pd ~/path/to/patch.pd
Thanks Max, that's what I already did in the call to the debugger:
$ gdb --args LD_PRELOAD=LeapDeveloperKit_2.3.1+31549_linux/LeapSDK/lib/x64/libLeap.so /usr/bin/pd -path linux64bit Pd_leapmotion_0.1_mac/leap_motion_help.pd
Without debugger the external fails indeed without that line.